rs326626

Variant names:

• chr5-134276116-C-G
• rs326626
• ENST00000703317.1:n.183+26474G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000703317.1(ENSG00000273345):​n.183+26474G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,166 control chromosomes in the GnomAD database, including 1,835 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 0.14 (1835 hom., cov: 32)
• Consequence: ENSG00000273345 ENST00000703317.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196

Genes affected

ENSG00000273345 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 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
ENSG00000273345	ENST00000703317.1	n.183+26474G>C		intron_variant	Intron 3 of 9			ENSP00000515260.1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21313 AN: 152048 Hom.: 1826 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0560

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0812

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.140 AC: 21349 AN: 152166 Hom.: 1835 Cov.: 32 AF XY: 0.146 AC XY: 10833 AN XY: 74390

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.0556

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.0812

Gnomad4 OTH AF: 0.168

Alfa AF: 0.115 Hom.: 147

Bravo AF: 0.148

Asia WGS AF: 0.120 AC: 416 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	5.8
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs326626; hg19: chr5-133611807;