rs10520437

Variant names:

• chr4-179842816-A-G
• rs10520437

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 0.233 in 152,046 control chromosomes in the GnomAD database, including 4,360 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 0.23 (4360 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.628
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.258 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: 0.233 AC: 35460 AN: 151928 Hom.: 4359 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.0726

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.233 AC: 35476 AN: 152046 Hom.: 4360 Cov.: 32 AF XY: 0.229 AC XY: 17013 AN XY: 74328

African (AFR) AF: 0.210 AC: 8724 AN: 41458

American (AMR) AF: 0.185 AC: 2828 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1412 AN: 3470

East Asian (EAS) AF: 0.0724 AC: 375 AN: 5180

South Asian (SAS) AF: 0.177 AC: 854 AN: 4824

European-Finnish (FIN) AF: 0.246 AC: 2600 AN: 10568

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17736 AN: 67966

Other (OTH) AF: 0.255 AC: 536 AN: 2106

Alfa AF: 0.257 Hom.: 2691

Bravo AF: 0.229

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.2
DANN	Benign	0.78
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs10520437; hg19: chr4-180763969;