chr4-130140798-T-C

Variant names:

• chr4-130140798-T-C
• rs2172478

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.706 in 151,216 control chromosomes in the GnomAD database, including 38,020 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 0.71 (38020 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 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: 0.706 AC: 106667 AN: 151098 Hom.: 37984 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.706 AC: 106753 AN: 151216 Hom.: 38020 Cov.: 32 AF XY: 0.699 AC XY: 51619 AN XY: 73878

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.709

Alfa AF: 0.689 Hom.: 3689

Bravo AF: 0.707

Asia WGS AF: 0.519 AC: 1804 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2172478; hg19: chr4-131061953;