rs17652343

Variant names:

• chr17-34245836-A-G
• rs17652343
• ENST00000776537.1:n.238+6037T>C

Variant summary

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

The ENST00000776537.1(ENSG00000301139):​n.238+6037T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,232 control chromosomes in the GnomAD database, including 2,299 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 0.16 (2299 hom., cov: 32)
• Consequence: ENSG00000301139 ENST00000776537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.754
• Publications: 6 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 (NFE) allele frequency at 95% confidence interval = 0.215 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+6037T>C		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776538.1	n.238+6037T>C		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776539.1	n.236+6037T>C		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776540.1	n.158+6037T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24652 AN: 152114 Hom.: 2298 Cov.: 32

Gnomad AFR AF: 0.0917

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.0780

Gnomad SAS AF: 0.0936

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.162 AC: 24659 AN: 152232 Hom.: 2299 Cov.: 32 AF XY: 0.158 AC XY: 11767 AN XY: 74430

African (AFR) AF: 0.0916 AC: 3806 AN: 41546

American (AMR) AF: 0.117 AC: 1784 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3470

East Asian (EAS) AF: 0.0778 AC: 403 AN: 5182

South Asian (SAS) AF: 0.0939 AC: 453 AN: 4824

European-Finnish (FIN) AF: 0.207 AC: 2198 AN: 10606

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14840 AN: 67988

Other (OTH) AF: 0.143 AC: 302 AN: 2110

Alfa AF: 0.196 Hom.: 5212

Bravo AF: 0.153

Asia WGS AF: 0.0840 AC: 294 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	3.4
DANN	Benign	0.78
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs17652343; hg19: chr17-32572855; COSMIC: COSV70609374;