chr4-125283761-C-T

Variant names:

• chr4-125283761-C-T
• rs10518462

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 0.177 in 152,064 control chromosomes in the GnomAD database, including 2,667 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 0.18 (2667 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.07
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 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: 0.177 AC: 26847 AN: 151946 Hom.: 2671 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0942

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.177 AC: 26874 AN: 152064 Hom.: 2667 Cov.: 32 AF XY: 0.172 AC XY: 12764 AN XY: 74354

African (AFR) AF: 0.259 AC: 10722 AN: 41464

American (AMR) AF: 0.177 AC: 2696 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3464

East Asian (EAS) AF: 0.0942 AC: 487 AN: 5170

South Asian (SAS) AF: 0.176 AC: 849 AN: 4820

European-Finnish (FIN) AF: 0.0730 AC: 773 AN: 10584

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10483 AN: 67984

Other (OTH) AF: 0.157 AC: 331 AN: 2108

Alfa AF: 0.167 Hom.: 306

Bravo AF: 0.189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.15
DANN	Benign	0.50
PhyloP100		-4.1

Splicing

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

Other links and lift over

dbSNP: rs10518462; hg19: chr4-126204916;