rs2516399

Positions:

• chr6-31513522-A-G

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 0.112 in 152,198 control chromosomes in the GnomAD database, including 1,093 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 (1093 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 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: 0.112 AC: 17071 AN: 152076 Hom.: 1092 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0845

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0590

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.112 AC: 17087 AN: 152198 Hom.: 1093 Cov.: 32 AF XY: 0.113 AC XY: 8402 AN XY: 74426

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.0845

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0590

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.121

Alfa AF: 0.107 Hom.: 1145

Bravo AF: 0.125

Asia WGS AF: 0.119 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2516399; hg19: chr6-31481299;