17-54186380-G-A

Variant names:

• chr17-54186380-G-A
• rs11079110
• ENST00000652614.1:n.294+31541C>T

Variant summary

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

The ENST00000652614.1(ENSG00000285939):​n.294+31541C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 152,010 control chromosomes in the GnomAD database, including 19,832 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 0.47 (19832 hom., cov: 32)
• Consequence: ENSG00000285939 ENST00000652614.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 0 publications found

Genes affected

ENSG00000285939 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.6 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
ENSG00000285939	ENST00000652614.1	n.294+31541C>T		intron_variant	Intron 2 of 2
ENSG00000302429	ENST00000786607.1	n.135+2901G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71937 AN: 151892 Hom.: 19831 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.473 AC: 71950 AN: 152010 Hom.: 19832 Cov.: 32 AF XY: 0.477 AC XY: 35441 AN XY: 74266

African (AFR) AF: 0.177 AC: 7329 AN: 41498

American (AMR) AF: 0.465 AC: 7097 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1971 AN: 3468

East Asian (EAS) AF: 0.543 AC: 2795 AN: 5152

South Asian (SAS) AF: 0.530 AC: 2553 AN: 4814

European-Finnish (FIN) AF: 0.683 AC: 7209 AN: 10558

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.605 AC: 41133 AN: 67950

Other (OTH) AF: 0.521 AC: 1098 AN: 2106

Alfa AF: 0.575 Hom.: 26077

Bravo AF: 0.447

Asia WGS AF: 0.496 AC: 1721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.77
DANN	Benign	0.42
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs11079110; hg19: chr17-52263741;