4-147424610-C-T

Variant names:

• chr4-147424610-C-T
• rs2115560

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 0.469 in 152,006 control chromosomes in the GnomAD database, including 19,959 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 0.47 (19959 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.675

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 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: 0.469 AC: 71300 AN: 151888 Hom.: 19961 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.469 AC: 71302 AN: 152006 Hom.: 19959 Cov.: 32 AF XY: 0.474 AC XY: 35178 AN XY: 74288

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.466

Alfa AF: 0.539 Hom.: 3064

Bravo AF: 0.446

Asia WGS AF: 0.432 AC: 1500 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
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: rs2115560; hg19: chr4-148345762;