ENST00000585572.1:n.380-1868C>T

Variant names:

• chr17-42559751-C-T
• rs12602084
• ENST00000585572.1:n.380-1868C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000585572.1(ENSG00000266929):​n.380-1868C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,022 control chromosomes in the GnomAD database, including 10,465 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 0.36 (10465 hom., cov: 31)
• Consequence: ENSG00000266929 ENST00000585572.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524

Genes affected

ENSG00000266929 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 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
ENSG00000266929	ENST00000585572.1	n.380-1868C>T		intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54309 AN: 151904 Hom.: 10471 Cov.: 31

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.357 AC: 54319 AN: 152022 Hom.: 10465 Cov.: 31 AF XY: 0.360 AC XY: 26753 AN XY: 74296

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.397

Alfa AF: 0.328 Hom.: 3493

Bravo AF: 0.358

Asia WGS AF: 0.375 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12602084; hg19: chr17-40711769;