rs2693364

Variant names:

• chr17-45574145-C-G
• rs2693364
• ENST00000686949.1:n.134+10427G>C

Variant summary

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

The ENST00000686949.1(ENSG00000291175):​n.134+10427G>C 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 (2173 hom., cov: 51)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000291175 ENST00000686949.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• 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=-0.93).

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+10427G>C		intron_variant	Intron 1 of 7
ENSG00000291175	ENST00000701132.2	n.134+10427G>C		intron_variant	Intron 1 of 2
ENSG00000291175	ENST00000717223.1	n.560+11557G>C		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65658 AN: 151046 Hom.: 2175 Cov.: 51

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.429

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: 65673 AN: 151166 Hom.: 2173 Cov.: 51 AF XY: 0.431 AC XY: 31804 AN XY: 73846

African (AFR) AF: 0.327 AC: 13443 AN: 41076

American (AMR) AF: 0.447 AC: 6762 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1757 AN: 3464

East Asian (EAS) AF: 0.317 AC: 1618 AN: 5110

South Asian (SAS) AF: 0.467 AC: 2242 AN: 4802

European-Finnish (FIN) AF: 0.429 AC: 4495 AN: 10486

Middle Eastern (MID) AF: 0.503 AC: 146 AN: 290

European-Non Finnish (NFE) AF: 0.498 AC: 33762 AN: 67800

Other (OTH) AF: 0.468 AC: 981 AN: 2096

Alfa AF: 0.457 Hom.: 299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.86
DANN	Benign	0.43
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2693364; hg19: chr17-43651511;