rs10520437

Positions:

• chr4-179842816-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.0724

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.255

Alfa AF: 0.255 Hom.: 2392

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520437; hg19: chr4-180763969;