rs10511142

Variant names:

• chr3-88813904-A-G
• rs10511142

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 0.1 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0241 AC: 1001 AN: 41472

American (AMR) AF: 0.273 AC: 4133 AN: 15130

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3458

East Asian (EAS) AF: 0.203 AC: 1039 AN: 5106

South Asian (SAS) AF: 0.122 AC: 589 AN: 4816

European-Finnish (FIN) AF: 0.0920 AC: 975 AN: 10596

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0972 AC: 6591 AN: 67794

Other (OTH) AF: 0.112 AC: 236 AN: 2100

Alfa AF: 0.0926 Hom.: 2190

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
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10511142; hg19: chr3-88863054;