4-124848462-G-T

Variant names:

• chr4-124848462-G-T
• rs13124340

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 0.106 in 152,092 control chromosomes in the GnomAD database, including 988 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 0.11 (988 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 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: 0.106 AC: 16161 AN: 151974 Hom.: 985 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.0791

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0858

Gnomad OTH AF: 0.0904

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

GnomAD4 genome AF: 0.106 AC: 16171 AN: 152092 Hom.: 988 Cov.: 32 AF XY: 0.110 AC XY: 8159 AN XY: 74320

African (AFR) AF: 0.127 AC: 5265 AN: 41492

American (AMR) AF: 0.0794 AC: 1213 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3468

East Asian (EAS) AF: 0.136 AC: 702 AN: 5174

South Asian (SAS) AF: 0.114 AC: 549 AN: 4828

European-Finnish (FIN) AF: 0.211 AC: 2222 AN: 10554

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0858 AC: 5832 AN: 67984

Other (OTH) AF: 0.0895 AC: 189 AN: 2112

Alfa AF: 0.0815 Hom.: 806

Bravo AF: 0.0987

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.83
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs13124340; hg19: chr4-125769617; COSMIC: COSV107200049;