rs17410962

Variant names:

• chr8-19990569-G-A
• rs17410962

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 0.145 in 152,148 control chromosomes in the GnomAD database, including 1,771 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 0.15 (1771 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464
• Publications: 40 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 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: 0.145 AC: 22107 AN: 152030 Hom.: 1771 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0988

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.145 AC: 22114 AN: 152148 Hom.: 1771 Cov.: 32 AF XY: 0.142 AC XY: 10587 AN XY: 74398

African (AFR) AF: 0.216 AC: 8952 AN: 41492

American (AMR) AF: 0.111 AC: 1692 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3472

East Asian (EAS) AF: 0.108 AC: 557 AN: 5178

South Asian (SAS) AF: 0.108 AC: 519 AN: 4812

European-Finnish (FIN) AF: 0.0988 AC: 1046 AN: 10582

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.122 AC: 8301 AN: 68006

Other (OTH) AF: 0.135 AC: 285 AN: 2112

Alfa AF: 0.132 Hom.: 2369

Bravo AF: 0.150

Asia WGS AF: 0.117 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.60
DANN	Benign	0.34
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs17410962; hg19: chr8-19848080;