17-34248740-T-C

Variant names:

• chr17-34248740-T-C
• rs2857653
• ENST00000776537.1:n.238+3133A>G

Variant summary

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

The ENST00000776537.1(ENSG00000301139):​n.238+3133A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.853 in 152,244 control chromosomes in the GnomAD database, including 55,751 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 0.85 (55751 hom., cov: 33)
• Consequence: ENSG00000301139 ENST00000776537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 9 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776537.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301139	ENST00000776537.1		n.238+3133A>G		intron	N/A
	ENSG00000301139	ENST00000776538.1		n.238+3133A>G		intron	N/A
	ENSG00000301139	ENST00000776539.1		n.236+3133A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.853 AC: 129728 AN: 152126 Hom.: 55688 Cov.: 33

Gnomad AFR AF: 0.954

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.829

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

GnomAD4 genome AF: 0.853 AC: 129851 AN: 152244 Hom.: 55751 Cov.: 33 AF XY: 0.856 AC XY: 63682 AN XY: 74420

African (AFR) AF: 0.954 AC: 39650 AN: 41552

American (AMR) AF: 0.795 AC: 12155 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2928 AN: 3472

East Asian (EAS) AF: 0.908 AC: 4711 AN: 5186

South Asian (SAS) AF: 0.917 AC: 4427 AN: 4828

European-Finnish (FIN) AF: 0.836 AC: 8847 AN: 10580

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54687 AN: 68010

Other (OTH) AF: 0.829 AC: 1752 AN: 2114

Alfa AF: 0.897 Hom.: 10673

Bravo AF: 0.850

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.78
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs2857653; hg19: chr17-32575759;