rs11080358

Positions:

• chr17-27803570-G-A

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/exons	MANE	Protein	UniProt
		n.27803570G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000266202	ENST00000582441.1	c.438+553C>T		intron_variant		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;