rs2693363

Variant names:

• chr17-45574056-T-C
• rs2693363
• ENST00000686949.1:n.134+10516A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000686949.1(ENSG00000291175):​n.134+10516A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.43 (2178 hom., cov: 53)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000291175 ENST00000686949.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.795
• Publications: 4 publications found

Genes affected

ENSG00000291175 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

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
ENSG00000291175	ENST00000686949.1	n.134+10516A>G		intron_variant	Intron 1 of 7
ENSG00000291175	ENST00000701132.2	n.134+10516A>G		intron_variant	Intron 1 of 2
ENSG00000291175	ENST00000717223.1	n.560+11646A>G		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65342 AN: 151076 Hom.: 2180 Cov.: 53

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.468

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.432 AC: 65356 AN: 151194 Hom.: 2178 Cov.: 53 AF XY: 0.429 AC XY: 31648 AN XY: 73838

African (AFR) AF: 0.326 AC: 13394 AN: 41118

American (AMR) AF: 0.444 AC: 6735 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1749 AN: 3458

East Asian (EAS) AF: 0.316 AC: 1623 AN: 5138

South Asian (SAS) AF: 0.466 AC: 2234 AN: 4794

European-Finnish (FIN) AF: 0.427 AC: 4476 AN: 10494

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.495 AC: 33561 AN: 67740

Other (OTH) AF: 0.467 AC: 973 AN: 2082

Alfa AF: 0.454 Hom.: 295

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.84
DANN	Benign	0.23
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs2693363; hg19: chr17-43651422;