17-27810524-A-G

Variant names:

• chr17-27810524-A-G
• rs2531863
• ENST00000582441.1:c.220-6183T>C

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.220-6183T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,752 control chromosomes in the GnomAD database, including 23,900 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 0.54 (23900 hom., cov: 33)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 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.220-6183T>C		intron	N/A	ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81486 AN: 151634 Hom.: 23904 Cov.: 33

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.537 AC: 81497 AN: 151752 Hom.: 23900 Cov.: 33 AF XY: 0.542 AC XY: 40200 AN XY: 74120

African (AFR) AF: 0.282 AC: 11694 AN: 41446

American (AMR) AF: 0.623 AC: 9506 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2035 AN: 3464

East Asian (EAS) AF: 0.744 AC: 3822 AN: 5140

South Asian (SAS) AF: 0.695 AC: 3347 AN: 4814

European-Finnish (FIN) AF: 0.630 AC: 6611 AN: 10498

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.628 AC: 42575 AN: 67830

Other (OTH) AF: 0.566 AC: 1195 AN: 2110

Alfa AF: 0.552 Hom.: 3099

Bravo AF: 0.527

Asia WGS AF: 0.677 AC: 2355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.55
PhyloP100		0.061

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: rs2531863; hg19: chr17-26137550;