rs728676

Variant names:

• chr5-118723839-A-G
• rs728676

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 0.405 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.256 AC: 10637 AN: 41496

American (AMR) AF: 0.367 AC: 5599 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1828 AN: 3470

East Asian (EAS) AF: 0.0883 AC: 457 AN: 5174

South Asian (SAS) AF: 0.448 AC: 2161 AN: 4822

European-Finnish (FIN) AF: 0.422 AC: 4458 AN: 10574

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34905 AN: 67970

Other (OTH) AF: 0.444 AC: 937 AN: 2108

Alfa AF: 0.479 Hom.: 30219

Bravo AF: 0.392

Asia WGS AF: 0.325 AC: 1131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.28
DANN	Benign	0.49
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs728676; hg19: chr5-118059534;