rs6931820

Variant names:

• chr6-93196655-G-A
• rs6931820

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 0.243 in 152,080 control chromosomes in the GnomAD database, including 5,343 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 0.24 (5343 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 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: 0.243 AC: 36894 AN: 151962 Hom.: 5339 Cov.: 32

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.243 AC: 36923 AN: 152080 Hom.: 5343 Cov.: 32 AF XY: 0.247 AC XY: 18390 AN XY: 74338

African (AFR) AF: 0.0881 AC: 3658 AN: 41510

American (AMR) AF: 0.321 AC: 4898 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 771 AN: 3470

East Asian (EAS) AF: 0.413 AC: 2134 AN: 5168

South Asian (SAS) AF: 0.252 AC: 1216 AN: 4818

European-Finnish (FIN) AF: 0.325 AC: 3434 AN: 10556

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19898 AN: 67968

Other (OTH) AF: 0.244 AC: 515 AN: 2108

Alfa AF: 0.269 Hom.: 9584

Bravo AF: 0.233

Asia WGS AF: 0.311 AC: 1079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.78
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs6931820; hg19: chr6-93906373; COSMIC: COSV69413760;