4-130091985-C-T

Position:

• chr4-130091985-C-T

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 0.552 in 152,072 control chromosomes in the GnomAD database, including 24,489 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 0.55 (24489 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 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: 0.551 AC: 83767 AN: 151954 Hom.: 24450 Cov.: 32

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.552 AC: 83872 AN: 152072 Hom.: 24489 Cov.: 32 AF XY: 0.550 AC XY: 40882 AN XY: 74330

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.553

Alfa AF: 0.483 Hom.: 31739

Bravo AF: 0.573

Asia WGS AF: 0.522 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.52
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11933661; hg19: chr4-131013140;