6-31383665-A-T

Position:

• chr6-31383665-A-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 0.707 in 152,178 control chromosomes in the GnomAD database, including 38,265 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 0.71 (38265 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.76 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: 0.707 AC: 107486 AN: 152060 Hom.: 38227 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.707 AC: 107577 AN: 152178 Hom.: 38265 Cov.: 32 AF XY: 0.705 AC XY: 52468 AN XY: 74388

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.735

Alfa AF: 0.707 Hom.: 4504

Bravo AF: 0.708

Asia WGS AF: 0.677 AC: 2356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.4
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3099848; hg19: chr6-31351442;