rs7729723

Variant names:

• chr5-138461691-A-G
• rs7729723

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 152,154 control chromosomes in the GnomAD database, including 13,020 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 (13020 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.474 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: 0.402 AC: 61109 AN: 152036 Hom.: 13007 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.456

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: 61155 AN: 152154 Hom.: 13020 Cov.: 33 AF XY: 0.402 AC XY: 29892 AN XY: 74384

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.423

Alfa AF: 0.441 Hom.: 20823

Bravo AF: 0.395

Asia WGS AF: 0.250 AC: 870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7729723; hg19: chr5-137797380;