rs6931820

chr6-93196655-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0881

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.244

Alfa AF: 0.275 Hom.: 7778

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

Splicing

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

Publications

LitVar

Other links and lift over

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