6-31090401-T-C

Variant names:

• chr6-31090401-T-C
• rs4947296

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 0.0684 in 149,622 control chromosomes in the GnomAD database, including 486 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 0.068 (486 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.538
• Publications: 62 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0686 AC: 10256 AN: 149524 Hom.: 490 Cov.: 32

Gnomad AFR AF: 0.0254

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0887

Gnomad ASJ AF: 0.0315

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0911

Gnomad MID AF: 0.103

Gnomad NFE AF: 0.0732

Gnomad OTH AF: 0.0705

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

GnomAD4 genome AF: 0.0684 AC: 10240 AN: 149622 Hom.: 486 Cov.: 32 AF XY: 0.0710 AC XY: 5184 AN XY: 72976

African (AFR) AF: 0.0253 AC: 1027 AN: 40648

American (AMR) AF: 0.0882 AC: 1333 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.0315 AC: 108 AN: 3434

East Asian (EAS) AF: 0.219 AC: 1106 AN: 5052

South Asian (SAS) AF: 0.132 AC: 628 AN: 4750

European-Finnish (FIN) AF: 0.0911 AC: 914 AN: 10030

Middle Eastern (MID) AF: 0.104 AC: 30 AN: 288

European-Non Finnish (NFE) AF: 0.0732 AC: 4924 AN: 67300

Other (OTH) AF: 0.0703 AC: 147 AN: 2092

Alfa AF: 0.0725 Hom.: 1771

Bravo AF: 0.0645

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.7
DANN	Benign	0.79
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs4947296; hg19: chr6-31058178;