rs4313476

chr10-31627761-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;