chr6-67688337-G-A

Variant names:

• chr6-67688337-G-A
• rs2493374

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 0.476 in 151,748 control chromosomes in the GnomAD database, including 18,658 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 0.48 (18658 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 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: 0.477 AC: 72261 AN: 151632 Hom.: 18644 Cov.: 30

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.476 AC: 72298 AN: 151748 Hom.: 18658 Cov.: 30 AF XY: 0.483 AC XY: 35814 AN XY: 74120

African (AFR) AF: 0.273 AC: 11298 AN: 41374

American (AMR) AF: 0.503 AC: 7664 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1660 AN: 3466

East Asian (EAS) AF: 0.775 AC: 3958 AN: 5104

South Asian (SAS) AF: 0.571 AC: 2748 AN: 4812

European-Finnish (FIN) AF: 0.587 AC: 6186 AN: 10532

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37204 AN: 67924

Other (OTH) AF: 0.506 AC: 1067 AN: 2108

Alfa AF: 0.503 Hom.: 2786

Bravo AF: 0.467

Asia WGS AF: 0.639 AC: 2218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.1
DANN	Benign	0.77
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2493374; hg19: chr6-68398230;