rs10479334

Variant names:

• chr5-105618627-C-T
• rs10479334

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 0.932 in 152,062 control chromosomes in the GnomAD database, including 66,149 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 0.93 (66149 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 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: 0.932 AC: 141652 AN: 151944 Hom.: 66093 Cov.: 31

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.936

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.937

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

GnomAD4 genome AF: 0.932 AC: 141767 AN: 152062 Hom.: 66149 Cov.: 31 AF XY: 0.930 AC XY: 69161 AN XY: 74334

African (AFR) AF: 0.964 AC: 40034 AN: 41520

American (AMR) AF: 0.922 AC: 14056 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.936 AC: 3245 AN: 3468

East Asian (EAS) AF: 0.966 AC: 4984 AN: 5162

South Asian (SAS) AF: 0.948 AC: 4576 AN: 4828

European-Finnish (FIN) AF: 0.890 AC: 9424 AN: 10588

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62312 AN: 67934

Other (OTH) AF: 0.938 AC: 1980 AN: 2112

Alfa AF: 0.922 Hom.: 176825

Bravo AF: 0.936

Asia WGS AF: 0.960 AC: 3338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.036
DANN	Benign	0.30
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs10479334; hg19: chr5-104954328;