rs10520495

Variant names:

• chr4-181437504-C-A
• rs10520495

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 0.13 in 152,168 control chromosomes in the GnomAD database, including 1,467 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 0.13 (1467 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 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: 0.130 AC: 19749 AN: 152052 Hom.: 1459 Cov.: 32

Gnomad AFR AF: 0.0985

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.130 AC: 19774 AN: 152168 Hom.: 1467 Cov.: 32 AF XY: 0.132 AC XY: 9851 AN XY: 74406

African (AFR) AF: 0.0988 AC: 4102 AN: 41530

American (AMR) AF: 0.203 AC: 3098 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3468

East Asian (EAS) AF: 0.276 AC: 1426 AN: 5162

South Asian (SAS) AF: 0.167 AC: 805 AN: 4818

European-Finnish (FIN) AF: 0.114 AC: 1203 AN: 10594

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8079 AN: 68000

Other (OTH) AF: 0.141 AC: 298 AN: 2114

Alfa AF: 0.125 Hom.: 168

Bravo AF: 0.134

Asia WGS AF: 0.208 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.8
DANN	Benign	0.80
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10520495; hg19: chr4-182358657;