rs2696639

Positions:

• chr17-45573674-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 (2177 hom., cov: 50)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.45573674T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000291175	ENST00000686949.1	n.134+10898A>G		intron_variant
ENSG00000291175	ENST00000701132.1	n.31+10898A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 65626 AN: 151054 Hom.: 2179 Cov.: 50 FAILED QC

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.469

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: 0.434 AC: 65639 AN: 151170 Hom.: 2177 Cov.: 50 AF XY: 0.430 AC XY: 31806 AN XY: 73898

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.469

Alfa AF: 0.457 Hom.: 301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2696639; hg19: chr17-43651040;