17-34245994-G-T

Variant names:

• chr17-34245994-G-T
• rs11652585
• ENST00000776537.1:n.238+5879C>A

Variant summary

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

The ENST00000776537.1(ENSG00000301139):​n.238+5879C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0564 in 152,308 control chromosomes in the GnomAD database, including 283 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 0.056 (283 hom., cov: 33)
• Consequence: ENSG00000301139 ENST00000776537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.905
• Publications: 5 publications found

Genes affected

ENSG00000301139 (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 (SAS) allele frequency at 95% confidence interval = 0.0875 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
ENSG00000301139	ENST00000776537.1	n.238+5879C>A		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776538.1	n.238+5879C>A		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776539.1	n.236+5879C>A		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776540.1	n.158+5879C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0565 AC: 8593 AN: 152190 Hom.: 282 Cov.: 33

Gnomad AFR AF: 0.0152

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0574

Gnomad ASJ AF: 0.0521

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0945

Gnomad FIN AF: 0.0665

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.0806

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0564 AC: 8592 AN: 152308 Hom.: 283 Cov.: 33 AF XY: 0.0566 AC XY: 4213 AN XY: 74476

African (AFR) AF: 0.0152 AC: 630 AN: 41566

American (AMR) AF: 0.0573 AC: 877 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0521 AC: 181 AN: 3472

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5190

South Asian (SAS) AF: 0.0946 AC: 457 AN: 4830

European-Finnish (FIN) AF: 0.0665 AC: 705 AN: 10606

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.0807 AC: 5487 AN: 68028

Other (OTH) AF: 0.0681 AC: 144 AN: 2116

Alfa AF: 0.0263 Hom.: 20

Bravo AF: 0.0537

Asia WGS AF: 0.0340 AC: 120 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	0.23
DANN	Benign	0.37
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs11652585; hg19: chr17-32573013;