17-27804344-G-T

Variant names:

• chr17-27804344-G-T
• rs2779252
• ENST00000582441.1:c.220-3C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000582441.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000266202	ENST00000582441.1	TSL:4	c.220-3C>A		splice_region intron	N/A	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

GnomAD2 exomes AF: 0.00 AC: 0 AN: 22 AF XY: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

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

African (AFR) AF: 0.0150 AC: 108 AN: 7180

American (AMR) AF: 0.0631 AC: 469 AN: 7436

Ashkenazi Jewish (ASJ) AF: 0.0564 AC: 521 AN: 9242

East Asian (EAS) AF: 0.263 AC: 6031 AN: 22894

South Asian (SAS) AF: 0.135 AC: 406 AN: 3014

European-Finnish (FIN) AF: 0.0582 AC: 1212 AN: 20824

Middle Eastern (MID) AF: 0.0772 AC: 100 AN: 1296

European-Non Finnish (NFE) AF: 0.0479 AC: 7576 AN: 158092

Other (OTH) AF: 0.0702 AC: 1149 AN: 16370

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

African (AFR) AF: 0.0134 AC: 559 AN: 41568

American (AMR) AF: 0.0561 AC: 858 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0562 AC: 195 AN: 3472

East Asian (EAS) AF: 0.304 AC: 1565 AN: 5152

South Asian (SAS) AF: 0.141 AC: 678 AN: 4818

European-Finnish (FIN) AF: 0.0552 AC: 586 AN: 10622

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0461 AC: 3137 AN: 68010

Other (OTH) AF: 0.0616 AC: 130 AN: 2112

Alfa AF: 0.0501 Hom.: 449

Bravo AF: 0.0514

Asia WGS AF: 0.181 AC: 627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	16
DANN	Benign	0.90
PhyloP100		2.3

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

Other links and lift over

dbSNP: rs2779252; hg19: chr17-26131370;