rs4703872

chr5-72427817-C-T

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 0.402 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.430

Alfa AF: 0.443 Hom.: 7905

Bravo AF: 0.390

Asia WGS AF: 0.657 AC: 2284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	7.7
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4703872; hg19: chr5-71723644;