rs17138064

Variant names:

• chr17-36831827-G-A
• rs17138064

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 0.0658 in 152,256 control chromosomes in the GnomAD database, including 486 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 0.066 (486 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 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: 0.0659 AC: 10024 AN: 152138 Hom.: 488 Cov.: 32

Gnomad AFR AF: 0.0165

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0745

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.0860

Gnomad FIN AF: 0.0786

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0781

Gnomad OTH AF: 0.0780

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

GnomAD4 genome AF: 0.0658 AC: 10016 AN: 152256 Hom.: 486 Cov.: 32 AF XY: 0.0673 AC XY: 5009 AN XY: 74446

African (AFR) AF: 0.0164 AC: 681 AN: 41556

American (AMR) AF: 0.0744 AC: 1137 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0798 AC: 277 AN: 3470

East Asian (EAS) AF: 0.209 AC: 1081 AN: 5178

South Asian (SAS) AF: 0.0852 AC: 411 AN: 4824

European-Finnish (FIN) AF: 0.0786 AC: 833 AN: 10604

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0781 AC: 5315 AN: 68016

Other (OTH) AF: 0.0772 AC: 163 AN: 2112

Alfa AF: 0.0730 Hom.: 827

Bravo AF: 0.0641

Asia WGS AF: 0.156 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.55
DANN	Benign	0.35
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs17138064; hg19: chr17-35189091;