chr6-49612845-A-G

Position:

• chr6-49612845-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000324.3(RHAG):​c.808-311T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,922 control chromosomes in the GnomAD database, including 8,047 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.32 (8047 hom., cov: 31)
• Consequence: RHAG NM_000324.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.21

Genes affected

RHAG (HGNC:10006): (Rh associated glycoprotein) The protein encoded by this gene is erythrocyte-specific and is thought to be part of a membrane channel that transports ammonium and carbon dioxide across the blood cell membrane. The encoded protein appears to interact with Rh blood group antigens and Rh30 polypeptides. Defects in this gene are a cause of regulator type Rh-null hemolytic anemia (RHN), or Rh-deficiency syndrome.[provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 6-49612845-A-G is Benign according to our data. Variant chr6-49612845-A-G is described in ClinVar as [Benign]. Clinvar id is 1296822.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RHAG	NM_000324.3	c.808-311T>C		intron_variant		ENST00000371175.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RHAG	ENST00000371175.10	c.808-311T>C		intron_variant		1	NM_000324.3	P2

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47979 AN: 151804 Hom.: 8041 Cov.: 31

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.310

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.316 AC: 48010 AN: 151922 Hom.: 8047 Cov.: 31 AF XY: 0.323 AC XY: 23983 AN XY: 74256

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.314

Alfa AF: 0.290 Hom.: 12447

Bravo AF: 0.322

Asia WGS AF: 0.459 AC: 1594 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.3
DANN	Benign	0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs1480617; hg19: chr6-49580558;