rs10513464

Variant names:

• chr3-154794323-G-T
• rs10513464

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 0.267 in 151,958 control chromosomes in the GnomAD database, including 6,266 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 0.27 (6266 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 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: 0.266 AC: 40455 AN: 151840 Hom.: 6243 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0199

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.267 AC: 40525 AN: 151958 Hom.: 6266 Cov.: 32 AF XY: 0.259 AC XY: 19255 AN XY: 74280

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.0196

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.246

Alfa AF: 0.246 Hom.: 2240

Bravo AF: 0.272

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513464; hg19: chr3-154512112;