rs10518632

Variant names:

• chr4-133246811-A-G
• rs10518632

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 0.0531 in 152,086 control chromosomes in the GnomAD database, including 256 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 0.053 (256 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.645
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0748 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: 0.0530 AC: 8062 AN: 151970 Hom.: 254 Cov.: 33

Gnomad AFR AF: 0.0770

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0567

Gnomad ASJ AF: 0.0285

Gnomad EAS AF: 0.0749

Gnomad SAS AF: 0.0630

Gnomad FIN AF: 0.0860

Gnomad MID AF: 0.0321

Gnomad NFE AF: 0.0316

Gnomad OTH AF: 0.0384

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

GnomAD4 genome AF: 0.0531 AC: 8077 AN: 152086 Hom.: 256 Cov.: 33 AF XY: 0.0569 AC XY: 4234 AN XY: 74346

African (AFR) AF: 0.0771 AC: 3202 AN: 41544

American (AMR) AF: 0.0568 AC: 867 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0285 AC: 99 AN: 3468

East Asian (EAS) AF: 0.0752 AC: 390 AN: 5184

South Asian (SAS) AF: 0.0631 AC: 304 AN: 4818

European-Finnish (FIN) AF: 0.0860 AC: 909 AN: 10566

Middle Eastern (MID) AF: 0.0276 AC: 8 AN: 290

European-Non Finnish (NFE) AF: 0.0316 AC: 2148 AN: 67932

Other (OTH) AF: 0.0385 AC: 81 AN: 2102

Alfa AF: 0.0462 Hom.: 23

Bravo AF: 0.0510

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.69
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs10518632; hg19: chr4-134167966;