17-27820226-T-C

Variant names:

• chr17-27820226-T-C
• rs2531872
• ENST00000582441.1:c.220-15885A>G

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.220-15885A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 152,086 control chromosomes in the GnomAD database, including 25,030 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 0.56 (25030 hom., cov: 33)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 8 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 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.220-15885A>G		intron_variant	Intron 3 of 4	4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84726 AN: 151968 Hom.: 25026 Cov.: 33

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.557 AC: 84761 AN: 152086 Hom.: 25030 Cov.: 33 AF XY: 0.562 AC XY: 41775 AN XY: 74342

African (AFR) AF: 0.352 AC: 14588 AN: 41498

American (AMR) AF: 0.631 AC: 9646 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2044 AN: 3470

East Asian (EAS) AF: 0.748 AC: 3863 AN: 5166

South Asian (SAS) AF: 0.692 AC: 3336 AN: 4822

European-Finnish (FIN) AF: 0.634 AC: 6693 AN: 10564

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42651 AN: 67966

Other (OTH) AF: 0.579 AC: 1221 AN: 2110

Alfa AF: 0.570 Hom.: 3345

Bravo AF: 0.548

Asia WGS AF: 0.685 AC: 2380 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.57
PhyloP100		-1.1

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: rs2531872; hg19: chr17-26147252;