rs2696640

Positions:

• chr17-45573867-G-A
• chr17-45573867-G-C

Variant summary

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

The ENST00000686949.1(ENSG00000291175):​n.134+10705C>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 (2182 hom., cov: 50)
  • Failed GnomAD Quality Control
• Consequence: ENST00000686949.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

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+10705C>T		intron_variant, non_coding_transcript_variant
	ENST00000701132.1	n.31+10705C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 65544 AN: 150978 Hom.: 2184 Cov.: 50 FAILED QC

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.428

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: 65556 AN: 151092 Hom.: 2182 Cov.: 50 AF XY: 0.430 AC XY: 31748 AN XY: 73792

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.468

Alfa AF: 0.260 Hom.: 67

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.40
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2696640; hg19: chr17-43651233;