rs10518620

chr4-132824452-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 0.0387 in 152,186 control chromosomes in the GnomAD database, including 269 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 0.039 (269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 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: 0.0386 AC: 5875 AN: 152068 Hom.: 268 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0170

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.0521

Gnomad SAS AF: 0.0133

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00756

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0387 AC: 5894 AN: 152186 Hom.: 269 Cov.: 32 AF XY: 0.0370 AC XY: 2756 AN XY: 74420

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.0169

Gnomad4 ASJ AF: 0.0228

Gnomad4 EAS AF: 0.0522

Gnomad4 SAS AF: 0.0131

Gnomad4 FIN AF: 0.00198

Gnomad4 NFE AF: 0.00756

Gnomad4 OTH AF: 0.0303

Alfa AF: 0.0255 Hom.: 18

Bravo AF: 0.0438

Asia WGS AF: 0.0400 AC: 139 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	7.6
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518620; hg19: chr4-133745607;