6-31600692-G-A

Variant names:

• chr6-31600692-G-A
• rs2857595

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 0.273 in 151,840 control chromosomes in the GnomAD database, including 6,552 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 0.27 (6552 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940
• Publications: 105 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41338 AN: 151722 Hom.: 6539 Cov.: 30

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.0950

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.273 AC: 41391 AN: 151840 Hom.: 6552 Cov.: 30 AF XY: 0.271 AC XY: 20080 AN XY: 74184

African (AFR) AF: 0.425 AC: 17557 AN: 41346

American (AMR) AF: 0.272 AC: 4143 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.0950 AC: 329 AN: 3464

East Asian (EAS) AF: 0.501 AC: 2586 AN: 5158

South Asian (SAS) AF: 0.172 AC: 829 AN: 4812

European-Finnish (FIN) AF: 0.186 AC: 1963 AN: 10572

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13244 AN: 67942

Other (OTH) AF: 0.238 AC: 503 AN: 2114

Alfa AF: 0.225 Hom.: 18147

Bravo AF: 0.286

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.57
PhyloP100		0.094

Splicing

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

Other links and lift over

dbSNP: rs2857595; hg19: chr6-31568469;