17-27804344-G-T

Position:

• chr17-27804344-G-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000582441.1(ENSG00000266202):​c.220-3C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0636 in 398,604 control chromosomes in the GnomAD database, including 1,618 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 0.051 (424 hom., cov: 32)
  • Exomes 𝑓: 0.071 (1194 hom.)
• Consequence: ENSG00000266202 ENST00000582441.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.27

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.27804344G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000266202	ENST00000582441.1	c.220-3C>A		splice_region_variant, intron_variant		4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.0511 AC: 7779 AN: 152140 Hom.: 423 Cov.: 32

Gnomad AFR AF: 0.0135

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0563

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0552

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0461

Gnomad OTH AF: 0.0603

GnomAD4 exome AF: 0.0713 AC: 17572 AN: 246348 Hom.: 1194 Cov.: 0 AF XY: 0.0703 AC XY: 8778 AN XY: 124828

Gnomad4 AFR exome AF: 0.0150

Gnomad4 AMR exome AF: 0.0631

Gnomad4 ASJ exome AF: 0.0564

Gnomad4 EAS exome AF: 0.263

Gnomad4 SAS exome AF: 0.135

Gnomad4 FIN exome AF: 0.0582

Gnomad4 NFE exome AF: 0.0479

Gnomad4 OTH exome AF: 0.0702

GnomAD4 genome AF: 0.0510 AC: 7772 AN: 152256 Hom.: 424 Cov.: 32 AF XY: 0.0538 AC XY: 4004 AN XY: 74448

Gnomad4 AFR AF: 0.0134

Gnomad4 AMR AF: 0.0561

Gnomad4 ASJ AF: 0.0562

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0552

Gnomad4 NFE AF: 0.0461

Gnomad4 OTH AF: 0.0616

Alfa AF: 0.0505 Hom.: 337

Bravo AF: 0.0514

Asia WGS AF: 0.181 AC: 627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	16
DANN	Benign	0.90

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.45		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.45		Position offset: -3

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

Publications

LitVar

Other links and lift over

dbSNP: rs2779252; hg19: chr17-26131370;