rs10511089

Variant names:

• chr3-84431917-G-T
• rs10511089

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 0.095 in 152,046 control chromosomes in the GnomAD database, including 848 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 0.095 (848 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.745
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.183 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: 0.0952 AC: 14456 AN: 151928 Hom.: 848 Cov.: 32

Gnomad AFR AF: 0.0306

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0939

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.0890

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0950 AC: 14449 AN: 152046 Hom.: 848 Cov.: 32 AF XY: 0.0961 AC XY: 7142 AN XY: 74324

African (AFR) AF: 0.0305 AC: 1268 AN: 41546

American (AMR) AF: 0.0938 AC: 1427 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3464

East Asian (EAS) AF: 0.193 AC: 994 AN: 5144

South Asian (SAS) AF: 0.0880 AC: 425 AN: 4828

European-Finnish (FIN) AF: 0.142 AC: 1501 AN: 10604

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8063 AN: 67936

Other (OTH) AF: 0.109 AC: 231 AN: 2112

Alfa AF: 0.112 Hom.: 3390

Bravo AF: 0.0892

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.3
DANN	Benign	0.75
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs10511089; hg19: chr3-84481068;