rs326626

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

ENSG00000273345 (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 (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000703317.1. 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
	ENSG00000273345	ENST00000703317.1		n.183+26474G>C		intron	N/A	ENSP00000515260.1	A0A8V8TQA6
	ENSG00000273345	ENST00000518409.2	TSL:2	n.904+26474G>C		intron	N/A
	ENSG00000273345	ENST00000520515.5	TSL:2	n.1226+26474G>C		intron	N/A

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

African (AFR) AF: 0.233 AC: 9663 AN: 41496

American (AMR) AF: 0.186 AC: 2838 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 409 AN: 3468

East Asian (EAS) AF: 0.0556 AC: 288 AN: 5180

South Asian (SAS) AF: 0.116 AC: 560 AN: 4830

European-Finnish (FIN) AF: 0.149 AC: 1575 AN: 10584

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0812 AC: 5520 AN: 68020

Other (OTH) AF: 0.168 AC: 353 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.8
DANN	Benign	0.72
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs326626;

hg19: chr5-133611807;