5-73482057-C-T

Variant names:

• chr5-73482057-C-T
• rs347247

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 0.821 in 152,124 control chromosomes in the GnomAD database, including 51,978 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 0.82 (51978 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.821 AC: 124764 AN: 152006 Hom.: 51920 Cov.: 30

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.821 AC: 124880 AN: 152124 Hom.: 51978 Cov.: 30 AF XY: 0.822 AC XY: 61147 AN XY: 74348

African (AFR) AF: 0.942 AC: 39108 AN: 41524

American (AMR) AF: 0.837 AC: 12796 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.816 AC: 2833 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5143 AN: 5158

South Asian (SAS) AF: 0.895 AC: 4312 AN: 4816

European-Finnish (FIN) AF: 0.709 AC: 7491 AN: 10562

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.742 AC: 50421 AN: 67982

Other (OTH) AF: 0.812 AC: 1717 AN: 2114

Alfa AF: 0.802 Hom.: 8048

Bravo AF: 0.837

Asia WGS AF: 0.941 AC: 3271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.51
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs347247; hg19: chr5-72777882;