5-173053333-C-T

Variant names:

• chr5-173053333-C-T
• rs251253
• ENST00000837003.1:n.96+946G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000837003.1(ENSG00000308874):​n.96+946G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 152,068 control chromosomes in the GnomAD database, including 20,601 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 0.50 (20601 hom., cov: 33)
• Consequence: ENSG00000308874 ENST00000837003.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 37 publications found

Genes affected

ENSG00000308874 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837003.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000308874	ENST00000837003.1		n.96+946G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76272 AN: 151950 Hom.: 20601 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.502 AC: 76319 AN: 152068 Hom.: 20601 Cov.: 33 AF XY: 0.500 AC XY: 37170 AN XY: 74324

African (AFR) AF: 0.355 AC: 14717 AN: 41462

American (AMR) AF: 0.434 AC: 6626 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1826 AN: 3472

East Asian (EAS) AF: 0.182 AC: 940 AN: 5176

South Asian (SAS) AF: 0.418 AC: 2018 AN: 4822

European-Finnish (FIN) AF: 0.672 AC: 7106 AN: 10574

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41392 AN: 67978

Other (OTH) AF: 0.498 AC: 1053 AN: 2116

Alfa AF: 0.555 Hom.: 95935

Bravo AF: 0.475

Asia WGS AF: 0.301 AC: 1046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.4
DANN	Benign	0.46
PhyloP100		0.037

Splicing

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

Other links and lift over

dbSNP: rs251253; hg19: chr5-172480336;