rs4313476

Variant names:

• chr10-31627761-T-C
• rs4313476

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.265 in 152,194 control chromosomes in the GnomAD database, including 6,574 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 (6574 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.29

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.37 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: 40412 AN: 152076 Hom.: 6574 Cov.: 33

Gnomad AFR AF: 0.0844

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.0951

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.265 AC: 40403 AN: 152194 Hom.: 6574 Cov.: 33 AF XY: 0.263 AC XY: 19594 AN XY: 74390

Gnomad4 AFR AF: 0.0841

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.0949

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.276

Alfa AF: 0.345 Hom.: 9630

Bravo AF: 0.254

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	15
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4313476; hg19: chr10-31916689;