rs728676

Variant names:

• chr5-118723839-A-G
• rs728676

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 0.405 in 152,080 control chromosomes in the GnomAD database, including 13,672 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 (13672 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.947

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.509 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: 0.405 AC: 61564 AN: 151962 Hom.: 13662 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.0881

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.405 AC: 61587 AN: 152080 Hom.: 13672 Cov.: 33 AF XY: 0.397 AC XY: 29498 AN XY: 74318

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.0883

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.444

Alfa AF: 0.489 Hom.: 24635

Bravo AF: 0.392

Asia WGS AF: 0.325 AC: 1131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.28
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs728676; hg19: chr5-118059534;