rs2350631

Positions:

• chr17-17600230-T-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, non coding transcript 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: ENST00000583662.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000583662.1	n.275+8528T>C		intron_variant, non_coding_transcript_variant		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;