17-39867188-T-G

Variant names:

• chr17-39867188-T-G
• rs1453560
• ENST00000789355.1:n.588A>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000789355.1(ENSG00000302760):​n.588A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.093 in 152,140 control chromosomes in the GnomAD database, including 1,344 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 0.093 (1344 hom., cov: 32)
• Consequence: ENSG00000302760 ENST00000789355.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.963
• Publications: 15 publications found

Genes affected

ENSG00000302760 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 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
ENSG00000302760	ENST00000789355.1	n.588A>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0927 AC: 14092 AN: 152022 Hom.: 1330 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0429

Gnomad ASJ AF: 0.00806

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.0394

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0368

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0930 AC: 14143 AN: 152140 Hom.: 1344 Cov.: 32 AF XY: 0.0910 AC XY: 6771 AN XY: 74416

African (AFR) AF: 0.248 AC: 10275 AN: 41444

American (AMR) AF: 0.0427 AC: 653 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00806 AC: 28 AN: 3472

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5192

South Asian (SAS) AF: 0.0176 AC: 85 AN: 4826

European-Finnish (FIN) AF: 0.0394 AC: 418 AN: 10610

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0369 AC: 2506 AN: 68002

Other (OTH) AF: 0.0758 AC: 160 AN: 2112

Alfa AF: 0.0541 Hom.: 1414

Bravo AF: 0.0995

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	17
DANN	Benign	0.73
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs1453560; hg19: chr17-38023441;