rs4313476

Variant names:

• chr10-31627761-T-C
• rs4313476

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0841 AC: 3494 AN: 41552

American (AMR) AF: 0.275 AC: 4202 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 900 AN: 3472

East Asian (EAS) AF: 0.0949 AC: 491 AN: 5174

South Asian (SAS) AF: 0.314 AC: 1516 AN: 4822

European-Finnish (FIN) AF: 0.305 AC: 3218 AN: 10564

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25444 AN: 67992

Other (OTH) AF: 0.276 AC: 584 AN: 2114

Alfa AF: 0.313 Hom.: 13016

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
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs4313476; hg19: chr10-31916689;