rs10518463

chr4-125312378-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 98 gene

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: 0.0339 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

Gnomad4 AFR AF: 0.00809

Gnomad4 AMR AF: 0.0322

Gnomad4 ASJ AF: 0.0260

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00953

Gnomad4 FIN AF: 0.0645

Gnomad4 NFE AF: 0.0499

Gnomad4 OTH AF: 0.0355

Alfa AF: 0.0362 Hom.: 14

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518463; hg19: chr4-126233533;