rs4319456

Variant names:

• chr10-81177374-C-G
• rs4319456

Your query was ambiguous. Multiple possible variants found:

• chr10-81177374-C-G
• chr10-81177374-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.744 in 151,968 control chromosomes in the GnomAD database, including 42,336 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 0.74 (42336 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 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: 0.745 AC: 113055 AN: 151850 Hom.: 42316 Cov.: 31

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.744 AC: 113124 AN: 151968 Hom.: 42336 Cov.: 31 AF XY: 0.742 AC XY: 55130 AN XY: 74266

African (AFR) AF: 0.741 AC: 30714 AN: 41448

American (AMR) AF: 0.731 AC: 11169 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.873 AC: 3031 AN: 3472

East Asian (EAS) AF: 0.874 AC: 4512 AN: 5164

South Asian (SAS) AF: 0.679 AC: 3277 AN: 4824

European-Finnish (FIN) AF: 0.710 AC: 7492 AN: 10546

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50249 AN: 67926

Other (OTH) AF: 0.788 AC: 1664 AN: 2112

Alfa AF: 0.646 Hom.: 1790

Bravo AF: 0.751

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.60
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs4319456; hg19: chr10-82937130;