rs17644943

Variant names:

• chr17-66911503-C-T
• rs17644943

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 0.0802 in 152,092 control chromosomes in the GnomAD database, including 519 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 0.080 (519 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0802 AC: 12187 AN: 151974 Hom.: 517 Cov.: 31

Gnomad AFR AF: 0.0864

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0962

Gnomad ASJ AF: 0.0951

Gnomad EAS AF: 0.0295

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0712

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0711

Gnomad OTH AF: 0.0747

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

GnomAD4 genome AF: 0.0802 AC: 12202 AN: 152092 Hom.: 519 Cov.: 31 AF XY: 0.0817 AC XY: 6078 AN XY: 74352

African (AFR) AF: 0.0863 AC: 3578 AN: 41472

American (AMR) AF: 0.0968 AC: 1478 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0951 AC: 330 AN: 3470

East Asian (EAS) AF: 0.0292 AC: 151 AN: 5176

South Asian (SAS) AF: 0.183 AC: 880 AN: 4806

European-Finnish (FIN) AF: 0.0712 AC: 754 AN: 10588

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0711 AC: 4837 AN: 67994

Other (OTH) AF: 0.0749 AC: 158 AN: 2110

Alfa AF: 0.0757 Hom.: 1360

Bravo AF: 0.0799

Asia WGS AF: 0.113 AC: 391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs17644943; hg19: chr17-64907620;