4-115244948-C-T

Position:

• chr4-115244948-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 0.598 in 151,258 control chromosomes in the GnomAD database, including 29,031 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 0.60 (29031 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.705 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: 0.598 AC: 90378 AN: 151146 Hom.: 29020 Cov.: 30

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.598 AC: 90418 AN: 151258 Hom.: 29031 Cov.: 30 AF XY: 0.599 AC XY: 44239 AN XY: 73876

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.619

Alfa AF: 0.637 Hom.: 5064

Bravo AF: 0.590

Asia WGS AF: 0.586 AC: 2028 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1112531; hg19: chr4-116166104;