rs17661538

Variant names:

• chr10-18108318-G-C
• rs17661538

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 0.129 in 151,990 control chromosomes in the GnomAD database, including 1,384 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 0.13 (1384 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 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: 0.129 AC: 19525 AN: 151870 Hom.: 1379 Cov.: 31

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.0627

Gnomad SAS AF: 0.0998

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.0999

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.129 AC: 19547 AN: 151990 Hom.: 1384 Cov.: 31 AF XY: 0.131 AC XY: 9730 AN XY: 74278

African (AFR) AF: 0.171 AC: 7084 AN: 41438

American (AMR) AF: 0.155 AC: 2361 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0617 AC: 214 AN: 3470

East Asian (EAS) AF: 0.0628 AC: 325 AN: 5172

South Asian (SAS) AF: 0.0989 AC: 476 AN: 4814

European-Finnish (FIN) AF: 0.173 AC: 1822 AN: 10524

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.0999 AC: 6795 AN: 67990

Other (OTH) AF: 0.125 AC: 263 AN: 2110

Alfa AF: 0.101 Hom.: 463

Bravo AF: 0.129

Asia WGS AF: 0.0790 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.67
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs17661538; hg19: chr10-18397247;