6-31353434-C-T

Position:

• chr6-31353434-C-T

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 0.567 in 151,816 control chromosomes in the GnomAD database, including 25,001 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 0.57 (25001 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.567 AC: 85964 AN: 151698 Hom.: 24971 Cov.: 30

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.567 AC: 86051 AN: 151816 Hom.: 25001 Cov.: 30 AF XY: 0.570 AC XY: 42315 AN XY: 74200

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.620

Alfa AF: 0.541 Hom.: 35676

Bravo AF: 0.585

Asia WGS AF: 0.653 AC: 2269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2596501; hg19: chr6-31321211;