rs17601696

Variant names:

• chr10-121360522-C-T
• rs17601696

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 0.0601 in 152,076 control chromosomes in the GnomAD database, including 382 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 0.060 (382 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0851 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: 0.0601 AC: 9136 AN: 151960 Hom.: 380 Cov.: 31

Gnomad AFR AF: 0.0147

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.0498

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0890

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0870

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.0601 AC: 9135 AN: 152076 Hom.: 382 Cov.: 31 AF XY: 0.0583 AC XY: 4337 AN XY: 74342

African (AFR) AF: 0.0147 AC: 610 AN: 41502

American (AMR) AF: 0.0497 AC: 760 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5176

South Asian (SAS) AF: 0.0224 AC: 108 AN: 4818

European-Finnish (FIN) AF: 0.0890 AC: 937 AN: 10524

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0870 AC: 5913 AN: 67996

Other (OTH) AF: 0.0838 AC: 177 AN: 2112

Alfa AF: 0.0753 Hom.: 604

Bravo AF: 0.0576

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.0
DANN	Benign	0.76
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs17601696; hg19: chr10-123120036;