rs2516463

chr6-31448759-A-Gchr6-31448759-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 0.107 in 151,916 control chromosomes in the GnomAD database, including 1,318 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 0.11 (1318 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 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: 0.107 AC: 16177 AN: 151798 Hom.: 1315 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0838

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.0858

Gnomad FIN AF: 0.0119

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.107 AC: 16196 AN: 151916 Hom.: 1318 Cov.: 33 AF XY: 0.104 AC XY: 7692 AN XY: 74286

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.0838

Gnomad4 EAS AF: 0.0102

Gnomad4 SAS AF: 0.0859

Gnomad4 FIN AF: 0.0119

Gnomad4 NFE AF: 0.0745

Gnomad4 OTH AF: 0.135

Alfa AF: 0.0699 Hom.: 291

Bravo AF: 0.121

Asia WGS AF: 0.0630 AC: 219 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	4.2
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2516463; hg19: chr6-31416536;