rs17635531

Variant names:

• chr3-143247876-G-A
• rs17635531

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 0.0512 in 152,304 control chromosomes in the GnomAD database, including 286 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 0.051 (286 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0765 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: 0.0513 AC: 7802 AN: 152186 Hom.: 286 Cov.: 32

Gnomad AFR AF: 0.0125

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0365

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00952

Gnomad FIN AF: 0.0987

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0783

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0512 AC: 7798 AN: 152304 Hom.: 286 Cov.: 32 AF XY: 0.0508 AC XY: 3782 AN XY: 74462

African (AFR) AF: 0.0125 AC: 519 AN: 41586

American (AMR) AF: 0.0365 AC: 558 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0487 AC: 169 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.00952 AC: 46 AN: 4830

European-Finnish (FIN) AF: 0.0987 AC: 1044 AN: 10582

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0782 AC: 5322 AN: 68026

Other (OTH) AF: 0.0511 AC: 108 AN: 2114

Alfa AF: 0.0624 Hom.: 218

Bravo AF: 0.0443

Asia WGS AF: 0.00433 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.2
DANN	Benign	0.77
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs17635531; hg19: chr3-142966718;