rs4311994

chr10-111143332-C-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 0.129 in 152,252 control chromosomes in the GnomAD database, including 1,400 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 0.13 (1400 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 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: 0.129 AC: 19585 AN: 152134 Hom.: 1400 Cov.: 33

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0553

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.129 AC: 19591 AN: 152252 Hom.: 1400 Cov.: 33 AF XY: 0.126 AC XY: 9366 AN XY: 74436

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0552

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.139

Alfa AF: 0.133 Hom.: 189

Bravo AF: 0.125

Asia WGS AF: 0.0470 AC: 166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.2
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4311994; hg19: chr10-112903090;