rs1531732

chr3-99355841-A-G

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 0.127 in 152,230 control chromosomes in the GnomAD database, including 2,698 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 (2698 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 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: 0.127 AC: 19316 AN: 152112 Hom.: 2685 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.0328

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0305

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0241

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.127 AC: 19377 AN: 152230 Hom.: 2698 Cov.: 32 AF XY: 0.127 AC XY: 9476 AN XY: 74424

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.0698

Gnomad4 ASJ AF: 0.0328

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0305

Gnomad4 NFE AF: 0.0241

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0699 Hom.: 185

Bravo AF: 0.138

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.54
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1531732; hg19: chr3-99074685;