rs10518463

Variant names:

• chr4-125312378-A-G
• rs10518463

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0339 in 152,132 control chromosomes in the GnomAD database, including 98 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 0.034 (98 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• 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).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0339 (5158/152132) while in subpopulation NFE AF = 0.0499 (3390/67926). AF 95% confidence interval is 0.0485. There are 98 homozygotes in GnomAd4. There are 2446 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 98 gene

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: 0.0339 AC: 5160 AN: 152016 Hom.: 98 Cov.: 32

Gnomad AFR AF: 0.00811

Gnomad AMI AF: 0.0441

Gnomad AMR AF: 0.0322

Gnomad ASJ AF: 0.0260

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00952

Gnomad FIN AF: 0.0645

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0499

Gnomad OTH AF: 0.0359

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

GnomAD4 genome AF: 0.0339 AC: 5158 AN: 152132 Hom.: 98 Cov.: 32 AF XY: 0.0329 AC XY: 2446 AN XY: 74360

African (AFR) AF: 0.00809 AC: 336 AN: 41548

American (AMR) AF: 0.0322 AC: 492 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0260 AC: 90 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.00953 AC: 46 AN: 4826

European-Finnish (FIN) AF: 0.0645 AC: 683 AN: 10584

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0499 AC: 3390 AN: 67926

Other (OTH) AF: 0.0355 AC: 75 AN: 2112

Alfa AF: 0.0278 Hom.: 21

Bravo AF: 0.0296

Asia WGS AF: 0.00521 AC: 18 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.78
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10518463; hg19: chr4-126233533;