ENST00000617914.2:n.357+2309T>C

Variant names:

• chr17-36150004-T-C
• rs1015673
• ENST00000617914.2:n.357+2309T>C

Variant summary

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

The ENST00000617914.2(ENSG00000276241):​n.357+2309T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 150,594 control chromosomes in the GnomAD database, including 12,638 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 0.40 (12638 hom., cov: 36)
• Consequence: ENSG00000276241 ENST00000617914.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.51
• Publications: 3 publications found

Genes affected

ENSG00000276241 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 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
ENSG00000276241	ENST00000617914.2	n.357+2309T>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.404 AC: 60857 AN: 150476 Hom.: 12639 Cov.: 36

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.404 AC: 60860 AN: 150594 Hom.: 12638 Cov.: 36 AF XY: 0.395 AC XY: 29085 AN XY: 73634

African (AFR) AF: 0.147 AC: 6021 AN: 40994

American (AMR) AF: 0.341 AC: 5160 AN: 15136

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1840 AN: 3446

East Asian (EAS) AF: 0.146 AC: 742 AN: 5090

South Asian (SAS) AF: 0.387 AC: 1843 AN: 4762

European-Finnish (FIN) AF: 0.486 AC: 5098 AN: 10496

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.574 AC: 38672 AN: 67378

Other (OTH) AF: 0.430 AC: 900 AN: 2092

Alfa AF: 0.503 Hom.: 4201

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs1015673; hg19: chr17-34477386;