rs2516049

Variant names:

• chr6-32602623-T-C
• rs2516049

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 0.27 in 151,676 control chromosomes in the GnomAD database, including 5,823 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 0.27 (5823 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 89 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.321 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: 0.270 AC: 40854 AN: 151560 Hom.: 5823 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.270 AC: 40878 AN: 151676 Hom.: 5823 Cov.: 31 AF XY: 0.264 AC XY: 19603 AN XY: 74152

African (AFR) AF: 0.215 AC: 8888 AN: 41354

American (AMR) AF: 0.328 AC: 5002 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1151 AN: 3464

East Asian (EAS) AF: 0.195 AC: 1007 AN: 5168

South Asian (SAS) AF: 0.247 AC: 1191 AN: 4820

European-Finnish (FIN) AF: 0.197 AC: 2072 AN: 10544

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.303 AC: 20523 AN: 67784

Other (OTH) AF: 0.279 AC: 590 AN: 2114

Alfa AF: 0.293 Hom.: 7232

Asia WGS AF: 0.211 AC: 734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.050
DANN	Benign	0.20
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2516049; hg19: chr6-32570400;