chr17-34225867-C-A

Variant names:

• chr17-34225867-C-A
• rs17652139
• ENST00000776537.1:n.239-6446G>T

Variant summary

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

The ENST00000776537.1(ENSG00000301139):​n.239-6446G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,160 control chromosomes in the GnomAD database, including 2,428 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 (2428 hom., cov: 33)
• Consequence: ENSG00000301139 ENST00000776537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450
• Publications: 8 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.219 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.239-6446G>T		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776538.1	n.239-2728G>T		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776539.1	n.237-2775G>T		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776540.1	n.159-2775G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25472 AN: 152040 Hom.: 2426 Cov.: 33

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.0787

Gnomad SAS AF: 0.0950

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.167 AC: 25482 AN: 152160 Hom.: 2428 Cov.: 33 AF XY: 0.163 AC XY: 12135 AN XY: 74384

African (AFR) AF: 0.102 AC: 4233 AN: 41530

American (AMR) AF: 0.122 AC: 1861 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 741 AN: 3470

East Asian (EAS) AF: 0.0785 AC: 407 AN: 5182

South Asian (SAS) AF: 0.0952 AC: 459 AN: 4820

European-Finnish (FIN) AF: 0.209 AC: 2205 AN: 10570

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15114 AN: 67990

Other (OTH) AF: 0.151 AC: 318 AN: 2112

Alfa AF: 0.135 Hom.: 325

Bravo AF: 0.159

Asia WGS AF: 0.0850 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.34
DANN	Benign	0.60
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs17652139; hg19: chr17-32552886; COSMIC: COSV70609373;