4-10151254-C-G

Variant names:

• chr4-10151254-C-G
• rs747357

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 0.423 in 151,954 control chromosomes in the GnomAD database, including 13,982 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 0.42 (13982 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 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: 0.422 AC: 64150 AN: 151836 Hom.: 13961 Cov.: 31

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.423 AC: 64214 AN: 151954 Hom.: 13982 Cov.: 31 AF XY: 0.418 AC XY: 31013 AN XY: 74254

African (AFR) AF: 0.382 AC: 15821 AN: 41416

American (AMR) AF: 0.448 AC: 6846 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2128 AN: 3472

East Asian (EAS) AF: 0.166 AC: 859 AN: 5160

South Asian (SAS) AF: 0.337 AC: 1626 AN: 4818

European-Finnish (FIN) AF: 0.400 AC: 4221 AN: 10556

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31230 AN: 67938

Other (OTH) AF: 0.445 AC: 936 AN: 2102

Alfa AF: 0.269 Hom.: 592

Bravo AF: 0.429

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.65
DANN	Benign	0.22
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs747357; hg19: chr4-10152878;