ENST00000582441.1:c.220-5883C>A

Variant names:

• chr17-27810224-G-T
• rs2779253
• ENST00000582441.1:c.220-5883C>A

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.220-5883C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,830 control chromosomes in the GnomAD database, including 24,053 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 (24053 hom., cov: 30)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 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.220-5883C>A		intron_variant	Intron 3 of 4	4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81717 AN: 151714 Hom.: 24058 Cov.: 30

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.538 AC: 81726 AN: 151830 Hom.: 24053 Cov.: 30 AF XY: 0.544 AC XY: 40364 AN XY: 74206

African (AFR) AF: 0.283 AC: 11695 AN: 41376

American (AMR) AF: 0.625 AC: 9532 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2039 AN: 3466

East Asian (EAS) AF: 0.745 AC: 3842 AN: 5156

South Asian (SAS) AF: 0.697 AC: 3346 AN: 4804

European-Finnish (FIN) AF: 0.633 AC: 6674 AN: 10544

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.629 AC: 42693 AN: 67922

Other (OTH) AF: 0.565 AC: 1191 AN: 2108

Alfa AF: 0.449 Hom.: 1536

Bravo AF: 0.527

Asia WGS AF: 0.677 AC: 2354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.77
PhyloP100		-0.30

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: rs2779253; hg19: chr17-26137250;