4-130140798-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;