6-76404370-G-A

Variant names:

• chr6-76404370-G-A
• rs2451563

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.459 in 151,890 control chromosomes in the GnomAD database, including 19,786 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 0.46 (19786 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69672 AN: 151770 Hom.: 19778 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.459 AC: 69694 AN: 151890 Hom.: 19786 Cov.: 31 AF XY: 0.456 AC XY: 33869 AN XY: 74228

African (AFR) AF: 0.114 AC: 4735 AN: 41460

American (AMR) AF: 0.512 AC: 7801 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2391 AN: 3464

East Asian (EAS) AF: 0.417 AC: 2146 AN: 5142

South Asian (SAS) AF: 0.551 AC: 2655 AN: 4818

European-Finnish (FIN) AF: 0.534 AC: 5637 AN: 10562

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42471 AN: 67894

Other (OTH) AF: 0.499 AC: 1053 AN: 2112

Alfa AF: 0.507 Hom.: 2859

Bravo AF: 0.446

Asia WGS AF: 0.429 AC: 1495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.50
PhyloP100		-0.024

Splicing

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

Other links and lift over

dbSNP: rs2451563; hg19: chr6-77114087; COSMIC: COSV69406001;