4-147472512-C-T

Variant names:

• chr4-147472512-C-T
• rs1878406

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 0.154 in 151,806 control chromosomes in the GnomAD database, including 1,805 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 0.15 (1805 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377
• Publications: 78 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 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: 0.154 AC: 23329 AN: 151688 Hom.: 1802 Cov.: 31

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.154 AC: 23345 AN: 151806 Hom.: 1805 Cov.: 31 AF XY: 0.154 AC XY: 11448 AN XY: 74224

African (AFR) AF: 0.179 AC: 7418 AN: 41350

American (AMR) AF: 0.130 AC: 1977 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 647 AN: 3468

East Asian (EAS) AF: 0.224 AC: 1153 AN: 5152

South Asian (SAS) AF: 0.185 AC: 891 AN: 4816

European-Finnish (FIN) AF: 0.141 AC: 1486 AN: 10560

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9264 AN: 67914

Other (OTH) AF: 0.146 AC: 307 AN: 2098

Alfa AF: 0.142 Hom.: 2882

Bravo AF: 0.157

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.44
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs1878406; hg19: chr4-148393664;