17-39756124-C-T

Variant names:

• chr17-39756124-C-T
• rs12946510
• ENST00000722328.1:n.1572C>T

Variant summary

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

The ENST00000722328.1(ENSG00000294270):​n.1572C>T 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 0.372 in 152,082 control chromosomes in the GnomAD database, including 11,648 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 0.37 (11648 hom., cov: 32)
• Consequence: ENSG00000294270 ENST00000722328.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 114 publications found

Genes affected

ENSG00000294270 (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 (NFE) allele frequency at 95% confidence interval = 0.448 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
ENSG00000294270	ENST00000722328.1	n.1572C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56536 AN: 151964 Hom.: 11644 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.372 AC: 56551 AN: 152082 Hom.: 11648 Cov.: 32 AF XY: 0.375 AC XY: 27859 AN XY: 74350

African (AFR) AF: 0.202 AC: 8363 AN: 41500

American (AMR) AF: 0.366 AC: 5592 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1491 AN: 3472

East Asian (EAS) AF: 0.292 AC: 1508 AN: 5156

South Asian (SAS) AF: 0.370 AC: 1787 AN: 4826

European-Finnish (FIN) AF: 0.533 AC: 5637 AN: 10580

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30734 AN: 67956

Other (OTH) AF: 0.357 AC: 754 AN: 2114

Alfa AF: 0.411 Hom.: 21213

Bravo AF: 0.347

Asia WGS AF: 0.371 AC: 1288 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	20
DANN	Benign	0.84
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs12946510; hg19: chr17-37912377;