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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000686949.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291175	ENST00000686949.1		n.134+10516A>G		intron	N/A
	ENSG00000291175	ENST00000701132.2		n.134+10516A>G		intron	N/A
	ENSG00000291175	ENST00000717223.1		n.560+11646A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2693363;

hg19: chr17-43651422;