chr5-73163239-C-T

Variant names:

• chr5-73163239-C-T
• rs1403728

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 0.581 in 152,014 control chromosomes in the GnomAD database, including 26,033 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 0.58 (26033 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 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: 0.582 AC: 88341 AN: 151896 Hom.: 26029 Cov.: 33

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.581 AC: 88388 AN: 152014 Hom.: 26033 Cov.: 33 AF XY: 0.581 AC XY: 43197 AN XY: 74292

African (AFR) AF: 0.502 AC: 20824 AN: 41468

American (AMR) AF: 0.626 AC: 9558 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2086 AN: 3470

East Asian (EAS) AF: 0.735 AC: 3803 AN: 5174

South Asian (SAS) AF: 0.716 AC: 3450 AN: 4818

European-Finnish (FIN) AF: 0.503 AC: 5300 AN: 10546

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.609 AC: 41386 AN: 67950

Other (OTH) AF: 0.606 AC: 1279 AN: 2112

Alfa AF: 0.598 Hom.: 74318

Bravo AF: 0.585

Asia WGS AF: 0.717 AC: 2492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.17
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1403728; hg19: chr5-72459066;