rs9313548

Variant names:

• chr5-171534296-C-T
• rs9313548
• ENST00000830528.1:n.244-20790C>T

Variant summary

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

The ENST00000830528.1(ENSG00000308026):​n.244-20790C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 152,004 control chromosomes in the GnomAD database, including 23,898 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 0.55 (23898 hom., cov: 32)
• Consequence: ENSG00000308026 ENST00000830528.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.577
• Publications: 3 publications found

Genes affected

ENSG00000308026 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.65 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
ENSG00000308026	ENST00000830528.1	n.244-20790C>T		intron_variant	Intron 1 of 3
ENSG00000308026	ENST00000830529.1	n.161-20790C>T		intron_variant	Intron 1 of 2
ENSG00000308026	ENST00000830530.1	n.80-20790C>T		intron_variant	Intron 1 of 4
ENSG00000308026	ENST00000830531.1	n.246-20790C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84141 AN: 151886 Hom.: 23854 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.554 AC: 84244 AN: 152004 Hom.: 23898 Cov.: 32 AF XY: 0.548 AC XY: 40717 AN XY: 74296

African (AFR) AF: 0.656 AC: 27221 AN: 41464

American (AMR) AF: 0.604 AC: 9219 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2073 AN: 3470

East Asian (EAS) AF: 0.346 AC: 1783 AN: 5150

South Asian (SAS) AF: 0.365 AC: 1761 AN: 4822

European-Finnish (FIN) AF: 0.510 AC: 5402 AN: 10584

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34784 AN: 67928

Other (OTH) AF: 0.590 AC: 1244 AN: 2110

Alfa AF: 0.524 Hom.: 11186

Bravo AF: 0.568

Asia WGS AF: 0.389 AC: 1354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.48
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs9313548; hg19: chr5-170961300;