rs728937

Variant names:

• chr5-147106119-T-C
• rs728937

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 0.42 in 151,950 control chromosomes in the GnomAD database, including 16,466 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 0.42 (16466 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.805
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63869 AN: 151832 Hom.: 16460 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.420 AC: 63883 AN: 151950 Hom.: 16466 Cov.: 32 AF XY: 0.422 AC XY: 31379 AN XY: 74276

African (AFR) AF: 0.119 AC: 4928 AN: 41378

American (AMR) AF: 0.484 AC: 7396 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1931 AN: 3466

East Asian (EAS) AF: 0.316 AC: 1622 AN: 5140

South Asian (SAS) AF: 0.528 AC: 2543 AN: 4818

European-Finnish (FIN) AF: 0.593 AC: 6269 AN: 10574

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37652 AN: 67978

Other (OTH) AF: 0.425 AC: 898 AN: 2112

Alfa AF: 0.503 Hom.: 62609

Bravo AF: 0.397

Asia WGS AF: 0.396 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.8
DANN	Benign	0.90
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs728937; hg19: chr5-146485682;