rs17635531

chr3-143247876-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0125

Gnomad4 AMR AF: 0.0365

Gnomad4 ASJ AF: 0.0487

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00952

Gnomad4 FIN AF: 0.0987

Gnomad4 NFE AF: 0.0782

Gnomad4 OTH AF: 0.0511

Alfa AF: 0.0688 Hom.: 131

Bravo AF: 0.0443

Asia WGS AF: 0.00433 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	5.2
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17635531; hg19: chr3-142966718;