6-31004812-G-T

Variant names:

• chr6-31004812-G-T
• rs1634717

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 0.387 in 152,052 control chromosomes in the GnomAD database, including 11,921 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 0.39 (11921 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367
• Publications: 33 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 (AMR) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58856 AN: 151934 Hom.: 11917 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.387 AC: 58892 AN: 152052 Hom.: 11921 Cov.: 32 AF XY: 0.377 AC XY: 28014 AN XY: 74324

African (AFR) AF: 0.323 AC: 13396 AN: 41440

American (AMR) AF: 0.455 AC: 6951 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2021 AN: 3468

East Asian (EAS) AF: 0.170 AC: 878 AN: 5178

South Asian (SAS) AF: 0.227 AC: 1095 AN: 4824

European-Finnish (FIN) AF: 0.331 AC: 3493 AN: 10556

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29694 AN: 67982

Other (OTH) AF: 0.426 AC: 901 AN: 2114

Alfa AF: 0.424 Hom.: 58586

Bravo AF: 0.402

Asia WGS AF: 0.242 AC: 841 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	3.3
DANN	Benign	0.79
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs1634717; hg19: chr6-30972589;