6-31094890-T-C

Position:

• chr6-31094890-T-C

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 0.658 in 151,396 control chromosomes in the GnomAD database, including 33,047 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 0.66 (33047 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99507 AN: 151278 Hom.: 33015 Cov.: 27

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.658 AC: 99580 AN: 151396 Hom.: 33047 Cov.: 27 AF XY: 0.656 AC XY: 48522 AN XY: 73942

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.692

Alfa AF: 0.639 Hom.: 34344

Bravo AF: 0.660

Asia WGS AF: 0.668 AC: 2327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.89
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2517448; hg19: chr6-31062667;