rs2696640

Variant names:

• chr17-45573867-G-A
• rs2696640
• ENST00000686949.1:n.134+10705C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-45573867-G-A
• chr17-45573867-G-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+10705C>T 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 (2182 hom., cov: 50)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000291175 ENST00000686949.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• 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=-0.9).

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+10705C>T		intron_variant	Intron 1 of 7
ENSG00000291175	ENST00000701132.2	n.134+10705C>T		intron_variant	Intron 1 of 2
ENSG00000291175	ENST00000717223.1	n.560+11835C>T		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65544 AN: 150978 Hom.: 2184 Cov.: 50

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

African (AFR) AF: 0.325 AC: 13348 AN: 41040

American (AMR) AF: 0.447 AC: 6775 AN: 15172

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

East Asian (EAS) AF: 0.316 AC: 1615 AN: 5114

South Asian (SAS) AF: 0.468 AC: 2244 AN: 4796

European-Finnish (FIN) AF: 0.428 AC: 4481 AN: 10462

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

European-Non Finnish (NFE) AF: 0.498 AC: 33747 AN: 67760

Other (OTH) AF: 0.468 AC: 978 AN: 2090

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2696640; hg19: chr17-43651233;