rs11036415

chr11-5241552-A-Cchr11-5241552-A-Gchr11-5241552-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000454892.2(ENSG00000290652):n.1003T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,058 control chromosomes in the GnomAD database, including 50,881 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.82 (50864 hom., cov: 30)
  • Exomes 𝑓: 0.81 (17 hom.)
• Consequence: ENST00000454892.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

(HGNC:):

HBD (HGNC:4829): (hemoglobin subunit delta) The delta (HBD) and beta (HBB) genes are normally expressed in the adult: two alpha chains plus two beta chains constitute HbA, which in normal adult life comprises about 97% of the total hemoglobin. Two alpha chains plus two delta chains constitute HbA-2, which with HbF comprises the remaining 3% of adult hemoglobin. Five beta-like globin genes are found within a 45 kb cluster on chromosome 11 in the following order: 5'-epsilon--Ggamma--Agamma--delta--beta-3'. Mutations in the delta-globin gene are associated with beta-thalassemia. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000454892.2	n.1003T>G		non_coding_transcript_exon_variant	3/3	2
HBD	ENST00000643122.1	c.-29+1898T>G		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124108 AN: 151886 Hom.: 50820 Cov.: 30

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.857

GnomAD4 exome AF: 0.815 AC: 44 AN: 54 Hom.: 17 Cov.: 0 AF XY: 0.813 AC XY: 26 AN XY: 32

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.833

Gnomad4 OTH exome AF: 0.833

GnomAD4 genome AF: 0.817 AC: 124214 AN: 152004 Hom.: 50864 Cov.: 30 AF XY: 0.813 AC XY: 60417 AN XY: 74298

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.863

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.860

Alfa AF: 0.816 Hom.: 10270

Bravo AF: 0.825

Asia WGS AF: 0.865 AC: 3008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.48
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11036415; hg19: chr11-5262782;