16-173135-T-C

Variant names:

• chr16-173135-T-C
• rs63750776
• NM_000517.6:c.106T>C

Variant summary

Our verdict is Likely pathogenic. The variant received 6 ACMG points: 6P and 0B. PM1 PP3_Moderate PP5_Moderate

The NM_000517.6(HBA2):​c.106T>C​(p.Ser36Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency: Genomes: not found (cov: 10)
• Consequence: HBA2 NM_000517.6 missense
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1 O:1
• Conservation: PhyloP100: -1.10
• Publications: 1 publications found

Genes affected

HBA2 (HGNC:4824): (hemoglobin subunit alpha 2) The human alpha globin gene cluster located on chromosome 16 spans about 30 kb and includes seven loci: 5'- zeta - pseudozeta - mu - pseudoalpha-1 - alpha-2 - alpha-1 - theta - 3'. The alpha-2 (HBA2) and alpha-1 (HBA1) coding sequences are identical. These genes differ slightly over the 5' untranslated regions and the introns, but they differ significantly over the 3' untranslated regions. Two alpha chains plus two beta chains constitute HbA, which in normal adult life comprises about 97% of the total hemoglobin; alpha chains combine with delta chains to constitute HbA-2, which with HbF (fetal hemoglobin) makes up the remaining 3% of adult hemoglobin. Alpha thalassemias result from deletions of each of the alpha genes as well as deletions of both HBA2 and HBA1; some nondeletion alpha thalassemias have also been reported. [provided by RefSeq, Jul 2008]

HBA2 Gene-Disease associations (from GenCC):

• alpha thalassemia spectrum

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen
• erythrocytosis, familial, 7

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
• hemoglobin M disease

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Hb Bart's hydrops fetalis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hemoglobin H disease

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Heinz body anemia

  Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
• methemoglobinemia, alpha type

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ENSG00000294455 (HGNC:):

ACMG classification

Our verdict: Likely_pathogenic. The variant received 6 ACMG points.

• PM1: In a hotspot region, there are 8 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 10 uncertain in NM_000517.6
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.905
• PP5: Variant 16-173135-T-C is Pathogenic according to our data. Variant chr16-173135-T-C is described in CliVar as Likely_pathogenic. Clinvar id is 993102.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-173135-T-C is described in CliVar as Likely_pathogenic. Clinvar id is 993102.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-173135-T-C is described in CliVar as Likely_pathogenic. Clinvar id is 993102.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-173135-T-C is described in CliVar as Likely_pathogenic. Clinvar id is 993102.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-173135-T-C is described in CliVar as Likely_pathogenic. Clinvar id is 993102.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HBA2	NM_000517.6	c.106T>C	p.Ser36Pro	missense_variant	Exon 2 of 3	ENST00000251595.11	NP_000508.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HBA2	ENST00000251595.11	c.106T>C	p.Ser36Pro	missense_variant	Exon 2 of 3	1	NM_000517.6	ENSP00000251595.6

Frequencies

GnomAD3 genomes Cov.: 10

GnomAD4 exome Cov.: 8

GnomAD4 genome Cov.: 10

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1 Other:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

Jan 13, 2021

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The variant has been reported as a variant having an alpha thalassemia-like phenotype. It has been observed in heterozygous carriers from a Portuguese family and associated with moderate erythrocytosis, microcytosis, and hypochromia (PMID: 17296578 (2007)). This variant was described as being unstable and causing Hb H disease in a severely affected infant with the Filipino deletional mutation (--FIL) on the other allele (PMID: 11722414 (2001)). This variant has not been reported in large, multi-ethnic general populations. -

HEMOGLOBIN H HYDROPS FETALIS SYNDROME Other:1

Oct 13, 2016

OMIM

Significance: other

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.30	D
BayesDel_noAF	Pathogenic	0.19
CADD	Benign	15
DANN	Uncertain	0.97
DEOGEN2	Benign	0.082	.;T
Eigen	Benign	-0.66
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.042	N
M_CAP	Pathogenic	0.57	D
MetaRNN	Pathogenic	0.91	D;D
MetaSVM	Uncertain	0.33	D
PhyloP100		-1.1
PrimateAI	Uncertain	0.64	T
PROVEAN	Uncertain	-3.0	D;D
REVEL	Uncertain	0.63
Sift	Uncertain	0.0020	D;D
Sift4G	Benign	0.088	T;T
Vest4		0.62
MutPred		0.78		Gain of glycosylation at T39 (P = 0.1011);.;
MVP		0.99
MPC		2.6
ClinPred		0.90	D
GERP RS		-8.3
PromoterAI		0.0030	Neutral
gMVP		0.95
Mutation Taster		=26/74	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs63750776; hg19: chr16-223134;