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).

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+10427G>C		intron	N/A
	ENSG00000291175	ENST00000701132.2		n.134+10427G>C		intron	N/A
	ENSG00000291175	ENST00000717223.1		n.560+11557G>C		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs2693364;

hg19: chr17-43651511;