5-158210268-C-T

Variant names:

• chr5-158210268-C-T
• rs202793
• ENST00000809623.1:n.177+34732C>T

Variant summary

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

The ENST00000809623.1(ENSG00000253673):​n.177+34732C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 151,300 control chromosomes in the GnomAD database, including 2,153 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 0.16 (2153 hom., cov: 30)
• Consequence: ENSG00000253673 ENST00000809623.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 2 publications found

Genes affected

ENSG00000253673 (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 (SAS) allele frequency at 95% confidence interval = 0.235 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
ENSG00000253673	ENST00000809623.1	n.177+34732C>T		intron_variant	Intron 1 of 1
ENSG00000253673	ENST00000809624.1	n.141+4020C>T		intron_variant	Intron 2 of 3
ENSG00000253673	ENST00000809625.1	n.39-31100C>T		intron_variant	Intron 1 of 1
ENSG00000253673	ENST00000809626.1	n.103+14162C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24832 AN: 151182 Hom.: 2144 Cov.: 30

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.164 AC: 24859 AN: 151300 Hom.: 2153 Cov.: 30 AF XY: 0.168 AC XY: 12420 AN XY: 73870

African (AFR) AF: 0.200 AC: 8226 AN: 41198

American (AMR) AF: 0.132 AC: 2002 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 506 AN: 3466

East Asian (EAS) AF: 0.220 AC: 1120 AN: 5102

South Asian (SAS) AF: 0.247 AC: 1180 AN: 4776

European-Finnish (FIN) AF: 0.164 AC: 1698 AN: 10380

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9567 AN: 67882

Other (OTH) AF: 0.169 AC: 354 AN: 2100

Alfa AF: 0.141 Hom.: 2603

Bravo AF: 0.159

Asia WGS AF: 0.285 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.37
DANN	Benign	0.63
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs202793; hg19: chr5-157637276;