rs10511321

chr3-113194658-T-C

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 0.039 in 152,272 control chromosomes in the GnomAD database, including 236 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 0.039 (236 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415

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 (AMR) allele frequency at 95% confidence interval = 0.0878 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: 0.0389 AC: 5917 AN: 152154 Hom.: 232 Cov.: 33

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0912

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.0389

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.00236

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00848

Gnomad OTH AF: 0.0512

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

GnomAD4 genome AF: 0.0390 AC: 5937 AN: 152272 Hom.: 236 Cov.: 33 AF XY: 0.0388 AC XY: 2892 AN XY: 74452

Gnomad4 AFR AF: 0.0803

Gnomad4 AMR AF: 0.0918

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.0388

Gnomad4 SAS AF: 0.0207

Gnomad4 FIN AF: 0.00236

Gnomad4 NFE AF: 0.00848

Gnomad4 OTH AF: 0.0502

Alfa AF: 0.0221 Hom.: 123

Bravo AF: 0.0499

Asia WGS AF: 0.0430 AC: 148 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	5.0
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: rs10511321; hg19: chr3-112913505;