6-31383258-T-C

Variant names:

• chr6-31383258-T-C
• rs2523485

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 0.874 in 152,260 control chromosomes in the GnomAD database, including 58,322 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 0.87 (58322 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 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: 0.874 AC: 133019 AN: 152142 Hom.: 58267 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.954

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.901

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

GnomAD4 genome AF: 0.874 AC: 133131 AN: 152260 Hom.: 58322 Cov.: 32 AF XY: 0.878 AC XY: 65383 AN XY: 74430

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.911

Gnomad4 ASJ AF: 0.957

Gnomad4 EAS AF: 0.972

Gnomad4 SAS AF: 0.954

Gnomad4 FIN AF: 0.872

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.902

Alfa AF: 0.870 Hom.: 28456

Bravo AF: 0.876

Asia WGS AF: 0.947 AC: 3295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.0
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2523485; hg19: chr6-31351035;