rs10520476

Positions:

• chr4-181353162-G-A

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 0.0241 in 152,104 control chromosomes in the GnomAD database, including 131 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 0.024 (131 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.983

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0241 AC: 3658 AN: 151986 Hom.: 130 Cov.: 32

Gnomad AFR AF: 0.0132

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0479

Gnomad FIN AF: 0.0600

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00579

Gnomad OTH AF: 0.0240

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

GnomAD4 genome AF: 0.0241 AC: 3668 AN: 152104 Hom.: 131 Cov.: 32 AF XY: 0.0281 AC XY: 2093 AN XY: 74362

Gnomad4 AFR AF: 0.0132

Gnomad4 AMR AF: 0.0706

Gnomad4 ASJ AF: 0.00663

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.0479

Gnomad4 FIN AF: 0.0600

Gnomad4 NFE AF: 0.00581

Gnomad4 OTH AF: 0.0247

Alfa AF: 0.0104 Hom.: 40

Bravo AF: 0.0249

Asia WGS AF: 0.0980 AC: 339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520476; hg19: chr4-182274315;