rs2350631

Variant names:

• chr17-17600230-T-C
• rs2350631
• ENST00000583662.1:n.275+8528T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000583662.1(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 ENST00000583662.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

Genes affected

ENSG00000264666 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	ENST00000583662.1	n.275+8528T>C		intron_variant	Intron 1 of 1	3

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

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.497

Alfa AF: 0.493 Hom.: 6243

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2350631; hg19: chr17-17503544;