rs723827

Variant names:

• chr5-116710102-G-C
• rs723827

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 0.0589 in 152,274 control chromosomes in the GnomAD database, including 761 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 0.059 (761 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 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: 0.0587 AC: 8938 AN: 152156 Hom.: 759 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0252

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.00642

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00791

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0589 AC: 8970 AN: 152274 Hom.: 761 Cov.: 32 AF XY: 0.0577 AC XY: 4293 AN XY: 74456

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.0252

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0222

Gnomad4 FIN AF: 0.00642

Gnomad4 NFE AF: 0.00791

Gnomad4 OTH AF: 0.0530

Alfa AF: 0.0353 Hom.: 54

Bravo AF: 0.0653

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs723827; hg19: chr5-116045798;