chr5-72427817-C-T

Variant names:

• chr5-72427817-C-T
• rs4703872

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 0.402 in 152,074 control chromosomes in the GnomAD database, including 13,975 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 0.40 (13975 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 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: 0.403 AC: 61192 AN: 151956 Hom.: 13975 Cov.: 33

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.402 AC: 61208 AN: 152074 Hom.: 13975 Cov.: 33 AF XY: 0.411 AC XY: 30542 AN XY: 74328

African (AFR) AF: 0.199 AC: 8261 AN: 41496

American (AMR) AF: 0.453 AC: 6922 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1425 AN: 3470

East Asian (EAS) AF: 0.874 AC: 4519 AN: 5168

South Asian (SAS) AF: 0.522 AC: 2517 AN: 4820

European-Finnish (FIN) AF: 0.518 AC: 5468 AN: 10552

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.452 AC: 30722 AN: 67980

Other (OTH) AF: 0.430 AC: 908 AN: 2114

Alfa AF: 0.443 Hom.: 8684

Bravo AF: 0.390

Asia WGS AF: 0.657 AC: 2284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	7.7
DANN	Benign	0.45
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs4703872; hg19: chr5-71723644;