rs2696639

Variant names:

• chr17-45573674-T-C
• rs2696639
• ENST00000686949.1:n.134+10898A>G

Variant summary

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

The ENST00000686949.1(ENSG00000291175):​n.134+10898A>G 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 (2177 hom., cov: 50)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000291175 ENST00000686949.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 3 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=-0.89).

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+10898A>G		intron_variant	Intron 1 of 7
ENSG00000291175	ENST00000701132.2	n.134+10898A>G		intron_variant	Intron 1 of 2
ENSG00000291175	ENST00000717223.1	n.560+12028A>G		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65626 AN: 151054 Hom.: 2179 Cov.: 50

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.427

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: 65639 AN: 151170 Hom.: 2177 Cov.: 50 AF XY: 0.430 AC XY: 31806 AN XY: 73898

African (AFR) AF: 0.327 AC: 13408 AN: 41022

American (AMR) AF: 0.446 AC: 6754 AN: 15130

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1755 AN: 3460

East Asian (EAS) AF: 0.316 AC: 1625 AN: 5138

South Asian (SAS) AF: 0.467 AC: 2247 AN: 4812

European-Finnish (FIN) AF: 0.427 AC: 4491 AN: 10506

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.498 AC: 33763 AN: 67804

Other (OTH) AF: 0.469 AC: 982 AN: 2096

Alfa AF: 0.457 Hom.: 301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.58
PhyloP100		0.091

Splicing

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

Other links and lift over

dbSNP: rs2696639; hg19: chr17-43651040;