4-71729084-C-T

Variant names:

• chr4-71729084-C-T
• rs13117483

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 0.231 in 152,082 control chromosomes in the GnomAD database, including 4,925 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 0.23 (4925 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 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: 0.231 AC: 35155 AN: 151964 Hom.: 4936 Cov.: 32

Gnomad AFR AF: 0.0938

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.231 AC: 35141 AN: 152082 Hom.: 4925 Cov.: 32 AF XY: 0.237 AC XY: 17611 AN XY: 74338

African (AFR) AF: 0.0935 AC: 3883 AN: 41516

American (AMR) AF: 0.284 AC: 4333 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 909 AN: 3470

East Asian (EAS) AF: 0.556 AC: 2870 AN: 5162

South Asian (SAS) AF: 0.428 AC: 2059 AN: 4814

European-Finnish (FIN) AF: 0.279 AC: 2942 AN: 10554

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17333 AN: 67978

Other (OTH) AF: 0.245 AC: 517 AN: 2108

Alfa AF: 0.249 Hom.: 2476

Bravo AF: 0.225

Asia WGS AF: 0.440 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.73
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs13117483; hg19: chr4-72594801;