rs17231602

Variant names:

• chr10-68252532-G-A
• rs17231602

Your query was ambiguous. Multiple possible variants found:

• chr10-68252532-G-A
• chr10-68252532-G-C

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 0.12 in 152,150 control chromosomes in the GnomAD database, including 1,493 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 0.12 (1493 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.797
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.21 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: 0.121 AC: 18322 AN: 152032 Hom.: 1493 Cov.: 32

Gnomad AFR AF: 0.0272

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.120 AC: 18331 AN: 152150 Hom.: 1493 Cov.: 32 AF XY: 0.126 AC XY: 9363 AN XY: 74376

African (AFR) AF: 0.0271 AC: 1125 AN: 41522

American (AMR) AF: 0.194 AC: 2965 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 630 AN: 3466

East Asian (EAS) AF: 0.148 AC: 765 AN: 5168

South Asian (SAS) AF: 0.221 AC: 1063 AN: 4818

European-Finnish (FIN) AF: 0.183 AC: 1936 AN: 10564

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9409 AN: 68016

Other (OTH) AF: 0.122 AC: 258 AN: 2110

Alfa AF: 0.140 Hom.: 946

Bravo AF: 0.118

Asia WGS AF: 0.163 AC: 569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.6
DANN	Benign	0.58
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs17231602; hg19: chr10-70012289;