ENST00000558550.2:n.1141-16366G>A

Variant names:

• chr15-84148033-G-A
• rs11635160
• ENST00000558550.2:n.1141-16366G>A

Variant summary

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

The ENST00000558550.2(ENSG00000291062):​n.1141-16366G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,130 control chromosomes in the GnomAD database, including 2,507 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 0.17 (2507 hom., cov: 30)
• Consequence: ENSG00000291062 ENST00000558550.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 6 publications found

Genes affected

ENSG00000291062 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558550.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291062	ENST00000558550.2	TSL:3	n.1141-16366G>A		intron	N/A
	ENSG00000291062	ENST00000560381.2	TSL:3	n.706+21433G>A		intron	N/A
	ENSG00000291062	ENST00000701714.2		n.1386-16366G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26186 AN: 152012 Hom.: 2509 Cov.: 30

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0439

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.172 AC: 26184 AN: 152130 Hom.: 2507 Cov.: 30 AF XY: 0.171 AC XY: 12693 AN XY: 74376

African (AFR) AF: 0.112 AC: 4652 AN: 41514

American (AMR) AF: 0.161 AC: 2456 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 570 AN: 3464

East Asian (EAS) AF: 0.0436 AC: 226 AN: 5182

South Asian (SAS) AF: 0.204 AC: 983 AN: 4818

European-Finnish (FIN) AF: 0.217 AC: 2297 AN: 10572

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14465 AN: 67992

Other (OTH) AF: 0.204 AC: 431 AN: 2110

Alfa AF: 0.187 Hom.: 352

Bravo AF: 0.166

Asia WGS AF: 0.115 AC: 400 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.026
DANN	Benign	0.55
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs11635160; hg19: chr15-84816785;