17-27807209-C-T

Variant names:

• chr17-27807209-C-T
• rs9902311
• ENST00000582441.1:c.220-2868G>A

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.220-2868G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 151,690 control chromosomes in the GnomAD database, including 5,799 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 0.27 (5799 hom., cov: 31)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.836
• Publications: 1 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.348 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.220-2868G>A		intron_variant	Intron 3 of 4	4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40943 AN: 151572 Hom.: 5795 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.270 AC: 40970 AN: 151690 Hom.: 5799 Cov.: 31 AF XY: 0.275 AC XY: 20411 AN XY: 74128

African (AFR) AF: 0.201 AC: 8309 AN: 41334

American (AMR) AF: 0.356 AC: 5434 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 935 AN: 3468

East Asian (EAS) AF: 0.263 AC: 1350 AN: 5126

South Asian (SAS) AF: 0.349 AC: 1680 AN: 4812

European-Finnish (FIN) AF: 0.315 AC: 3302 AN: 10476

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19064 AN: 67902

Other (OTH) AF: 0.260 AC: 549 AN: 2108

Alfa AF: 0.237 Hom.: 1595

Bravo AF: 0.267

Asia WGS AF: 0.324 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.36
PhyloP100		-0.84

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: rs9902311; hg19: chr17-26134235;