4-147424610-C-T

Variant names:

• chr4-147424610-C-T
• rs2115560

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.149 AC: 6196 AN: 41468

American (AMR) AF: 0.531 AC: 8108 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1848 AN: 3472

East Asian (EAS) AF: 0.601 AC: 3108 AN: 5170

South Asian (SAS) AF: 0.435 AC: 2101 AN: 4828

European-Finnish (FIN) AF: 0.671 AC: 7061 AN: 10530

Middle Eastern (MID) AF: 0.483 AC: 140 AN: 290

European-Non Finnish (NFE) AF: 0.607 AC: 41231 AN: 67956

Other (OTH) AF: 0.466 AC: 984 AN: 2110

Alfa AF: 0.524 Hom.: 3073

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
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs2115560; hg19: chr4-148345762;