4-141521637-C-T

Variant names:

• chr4-141521637-C-T
• rs4956396

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 0.198 in 152,086 control chromosomes in the GnomAD database, including 3,112 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 0.20 (3112 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.255 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: 0.197 AC: 29986 AN: 151966 Hom.: 3096 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.198 AC: 30057 AN: 152086 Hom.: 3112 Cov.: 32 AF XY: 0.198 AC XY: 14702 AN XY: 74346

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.201

Alfa AF: 0.129 Hom.: 284

Bravo AF: 0.207

Asia WGS AF: 0.207 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4956396; hg19: chr4-142442790;