chr6-31090401-T-C

Variant names:

• chr6-31090401-T-C
• rs4947296

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 0.0684 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0686 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

Gnomad4 AFR AF: 0.0253

Gnomad4 AMR AF: 0.0882

Gnomad4 ASJ AF: 0.0315

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0911

Gnomad4 NFE AF: 0.0732

Gnomad4 OTH AF: 0.0703

Alfa AF: 0.0745 Hom.: 675

Bravo AF: 0.0645

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4947296; hg19: chr6-31058178;