ENST00000666016.1:n.81+18767T>C

Variant names:

• chr17-15085670-A-G
• rs12603925
• ENST00000666016.1:n.81+18767T>C

Variant summary

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

The ENST00000666016.1(ENSG00000287307):​n.81+18767T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 152,058 control chromosomes in the GnomAD database, including 16,485 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 0.46 (16485 hom., cov: 33)
• Consequence: ENSG00000287307 ENST00000666016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 2 publications found

Genes affected

ENSG00000287307 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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
ENSG00000287307	ENST00000666016.1	n.81+18767T>C		intron_variant	Intron 1 of 1
ENSG00000306201	ENST00000816239.1	n.*85A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69871 AN: 151938 Hom.: 16483 Cov.: 33

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.460 AC: 69905 AN: 152058 Hom.: 16485 Cov.: 33 AF XY: 0.462 AC XY: 34365 AN XY: 74322

African (AFR) AF: 0.369 AC: 15318 AN: 41480

American (AMR) AF: 0.482 AC: 7370 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2120 AN: 3472

East Asian (EAS) AF: 0.580 AC: 3003 AN: 5176

South Asian (SAS) AF: 0.549 AC: 2646 AN: 4818

European-Finnish (FIN) AF: 0.452 AC: 4774 AN: 10560

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32940 AN: 67956

Other (OTH) AF: 0.488 AC: 1031 AN: 2112

Alfa AF: 0.456 Hom.: 7422

Bravo AF: 0.459

Asia WGS AF: 0.564 AC: 1963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.082
DANN	Benign	0.49
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs12603925; hg19: chr17-14988987;