rs2736189

Variant names:

• chr6-31596951-G-A
• rs2736189

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 0.107 in 152,034 control chromosomes in the GnomAD database, including 985 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 (985 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.134 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: 0.107 AC: 16316 AN: 151918 Hom.: 986 Cov.: 32

Gnomad AFR AF: 0.0611

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0991

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.0791

Gnomad SAS AF: 0.0844

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.107 AC: 16323 AN: 152034 Hom.: 985 Cov.: 32 AF XY: 0.106 AC XY: 7896 AN XY: 74324

African (AFR) AF: 0.0610 AC: 2528 AN: 41476

American (AMR) AF: 0.0993 AC: 1513 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3470

East Asian (EAS) AF: 0.0792 AC: 410 AN: 5174

South Asian (SAS) AF: 0.0843 AC: 405 AN: 4802

European-Finnish (FIN) AF: 0.137 AC: 1452 AN: 10574

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9270 AN: 67978

Other (OTH) AF: 0.123 AC: 260 AN: 2110

Alfa AF: 0.121 Hom.: 401

Bravo AF: 0.105

Asia WGS AF: 0.0930 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.3
DANN	Benign	0.89
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs2736189; hg19: chr6-31564728;