ENST00000583662.2:n.275+8528T>C

Variant names:

• chr17-17600230-T-C
• rs2350631
• ENST00000583662.2:n.275+8528T>C

Variant summary

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

The ENST00000583662.2(ENSG00000264666):​n.275+8528T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,822 control chromosomes in the GnomAD database, including 18,586 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 0.49 (18586 hom., cov: 31)
• Consequence: ENSG00000264666 ENST00000583662.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 2 publications found

Genes affected

ENSG00000264666 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 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
ENSG00000264666	ENST00000583662.2	n.275+8528T>C		intron_variant	Intron 1 of 1	3
ENSG00000264666	ENST00000816800.1	n.203+8528T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74411 AN: 151704 Hom.: 18576 Cov.: 31

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.490 AC: 74466 AN: 151822 Hom.: 18586 Cov.: 31 AF XY: 0.482 AC XY: 35771 AN XY: 74190

African (AFR) AF: 0.491 AC: 20326 AN: 41382

American (AMR) AF: 0.414 AC: 6314 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2014 AN: 3466

East Asian (EAS) AF: 0.451 AC: 2330 AN: 5164

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4816

European-Finnish (FIN) AF: 0.514 AC: 5409 AN: 10518

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35289 AN: 67924

Other (OTH) AF: 0.497 AC: 1045 AN: 2104

Alfa AF: 0.500 Hom.: 10495

Bravo AF: 0.490

Asia WGS AF: 0.376 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.8
DANN	Benign	0.88
PhyloP100		-0.099

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2350631; hg19: chr17-17503544;