chr4-130091985-C-T

Variant names:

• chr4-130091985-C-T
• rs11933661

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;