6-137638917-G-A

Variant names:

• chr6-137638917-G-A
• rs9321624

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 0.435 in 151,782 control chromosomes in the GnomAD database, including 14,467 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 0.43 (14467 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 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: 0.435 AC: 65951 AN: 151664 Hom.: 14462 Cov.: 30

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.435 AC: 65972 AN: 151782 Hom.: 14467 Cov.: 30 AF XY: 0.439 AC XY: 32532 AN XY: 74138

African (AFR) AF: 0.367 AC: 15205 AN: 41378

American (AMR) AF: 0.418 AC: 6378 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1373 AN: 3464

East Asian (EAS) AF: 0.531 AC: 2739 AN: 5162

South Asian (SAS) AF: 0.441 AC: 2106 AN: 4776

European-Finnish (FIN) AF: 0.529 AC: 5569 AN: 10526

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31220 AN: 67904

Other (OTH) AF: 0.450 AC: 949 AN: 2108

Alfa AF: 0.449 Hom.: 2041

Bravo AF: 0.423

Asia WGS AF: 0.475 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.65
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs9321624; hg19: chr6-137960054; COSMIC: COSV60285510;