rs2619537

Variant names:

• chr6-15664182-A-G
• rs2619537

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 0.206 in 152,044 control chromosomes in the GnomAD database, including 4,433 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 0.21 (4433 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 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: 0.206 AC: 31335 AN: 151926 Hom.: 4438 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.0804

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.206 AC: 31347 AN: 152044 Hom.: 4433 Cov.: 31 AF XY: 0.201 AC XY: 14925 AN XY: 74352

African (AFR) AF: 0.399 AC: 16526 AN: 41416

American (AMR) AF: 0.212 AC: 3232 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3468

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5182

South Asian (SAS) AF: 0.111 AC: 536 AN: 4810

European-Finnish (FIN) AF: 0.0779 AC: 825 AN: 10592

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9322 AN: 67986

Other (OTH) AF: 0.189 AC: 398 AN: 2110

Alfa AF: 0.173 Hom.: 434

Bravo AF: 0.226

Asia WGS AF: 0.0700 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.62
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2619537; hg19: chr6-15664413;