17-27817713-C-T

Variant names:

• chr17-27817713-C-T
• rs1014025
• ENST00000582441.1:c.220-13372G>A

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.220-13372G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,974 control chromosomes in the GnomAD database, including 13,362 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 0.41 (13362 hom., cov: 31)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498
• Publications: 6 publications found

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.469 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
ENSG00000266202	ENST00000582441.1	c.220-13372G>A		intron_variant	Intron 3 of 4	4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62496 AN: 151858 Hom.: 13351 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.412 AC: 62541 AN: 151974 Hom.: 13362 Cov.: 31 AF XY: 0.414 AC XY: 30721 AN XY: 74268

African (AFR) AF: 0.307 AC: 12723 AN: 41444

American (AMR) AF: 0.478 AC: 7299 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1419 AN: 3466

East Asian (EAS) AF: 0.271 AC: 1400 AN: 5160

South Asian (SAS) AF: 0.428 AC: 2060 AN: 4818

European-Finnish (FIN) AF: 0.473 AC: 4985 AN: 10546

Middle Eastern (MID) AF: 0.317 AC: 92 AN: 290

European-Non Finnish (NFE) AF: 0.460 AC: 31262 AN: 67960

Other (OTH) AF: 0.412 AC: 870 AN: 2110

Alfa AF: 0.436 Hom.: 1798

Bravo AF: 0.404

Asia WGS AF: 0.374 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.1
DANN	Benign	0.79
PhyloP100		-0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1014025; hg19: chr17-26144739;