rs11080358

Variant names:

• chr17-27803570-G-A
• rs11080358
• ENST00000582441.1:c.438+553C>T

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.438+553C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,174 control chromosomes in the GnomAD database, including 1,664 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 (1664 hom., cov: 32)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.91

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 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
ENSG00000266202	ENST00000582441.1	c.438+553C>T		intron_variant	Intron 4 of 4	4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21548 AN: 152056 Hom.: 1663 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0822

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.142 AC: 21577 AN: 152174 Hom.: 1664 Cov.: 32 AF XY: 0.139 AC XY: 10311 AN XY: 74404

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.0102

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0822

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.145

Alfa AF: 0.138 Hom.: 2231

Bravo AF: 0.150

Asia WGS AF: 0.0760 AC: 265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11080358; hg19: chr17-26130596;