rs10518620

Variant names:

• chr4-132824452-A-G
• rs10518620

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;