rs10511142

chr3-88813904-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 0.1 in 151,678 control chromosomes in the GnomAD database, including 1,215 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 0.10 (1215 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.266 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: 0.100 AC: 15179 AN: 151562 Hom.: 1205 Cov.: 31

Gnomad AFR AF: 0.0242

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0920

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0972

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.100 AC: 15203 AN: 151678 Hom.: 1215 Cov.: 31 AF XY: 0.105 AC XY: 7761 AN XY: 74126

Gnomad4 AFR AF: 0.0241

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0920

Gnomad4 NFE AF: 0.0972

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0912 Hom.: 1075

Bravo AF: 0.116

Asia WGS AF: 0.173 AC: 600 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.99
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511142; hg19: chr3-88863054;