rs10511089

chr3-84431917-G-T

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 0.095 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0305

Gnomad4 AMR AF: 0.0938

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.0880

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.109

Alfa AF: 0.118 Hom.: 2398

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511089; hg19: chr3-84481068;