chr4-141469715-A-C

Variant names:

• chr4-141469715-A-C
• rs17354547

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 0.176 in 152,232 control chromosomes in the GnomAD database, including 2,492 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 0.18 (2492 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.247 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: 0.176 AC: 26753 AN: 152114 Hom.: 2487 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.176 AC: 26790 AN: 152232 Hom.: 2492 Cov.: 32 AF XY: 0.177 AC XY: 13151 AN XY: 74432

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.186

Alfa AF: 0.186 Hom.: 670

Bravo AF: 0.183

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.1
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17354547; hg19: chr4-142390869;