rs2516399

Variant names:

• chr6-31513522-A-G
• rs2516399

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 35 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.106 AC: 4387 AN: 41522

American (AMR) AF: 0.201 AC: 3068 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0845 AC: 293 AN: 3466

East Asian (EAS) AF: 0.153 AC: 792 AN: 5174

South Asian (SAS) AF: 0.122 AC: 589 AN: 4826

European-Finnish (FIN) AF: 0.0590 AC: 625 AN: 10602

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7007 AN: 68008

Other (OTH) AF: 0.121 AC: 256 AN: 2108

Alfa AF: 0.110 Hom.: 3119

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
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs2516399; hg19: chr6-31481299;