rs2693371

Positions:

• chr17-45578322-C-A

Variant summary

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

The ENST00000686949.1(ENSG00000291175):​n.134+6250G>T variant causes a intron, non coding transcript 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 (2175 hom., cov: 52)
  • Failed GnomAD Quality Control
• Consequence: ENST00000686949.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000686949.1	n.134+6250G>T		intron_variant, non_coding_transcript_variant
	ENST00000701132.1	n.31+6250G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 65184 AN: 150980 Hom.: 2177 Cov.: 52 FAILED QC

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.498

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: 0.431 AC: 65196 AN: 151096 Hom.: 2175 Cov.: 52 AF XY: 0.428 AC XY: 31600 AN XY: 73868

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.468

Alfa AF: 0.455 Hom.: 300

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2693371; hg19: chr17-43655688; COSMIC: COSV69471729;