chr4-141469715-A-C

Variant names:

• chr4-141469715-A-C
• rs17354547

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 0.176 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.146 AC: 6067 AN: 41540

American (AMR) AF: 0.254 AC: 3874 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 637 AN: 3470

East Asian (EAS) AF: 0.221 AC: 1148 AN: 5184

South Asian (SAS) AF: 0.188 AC: 904 AN: 4816

European-Finnish (FIN) AF: 0.127 AC: 1348 AN: 10608

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12268 AN: 68018

Other (OTH) AF: 0.186 AC: 394 AN: 2114

Alfa AF: 0.186 Hom.: 685

Bravo AF: 0.183

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.1
DANN	Benign	0.87
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs17354547; hg19: chr4-142390869;