rs2693371

Variant names:

• chr17-45578322-C-A
• rs2693371
• ENST00000686949.1:n.134+6250G>T

Variant summary

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

The ENST00000686949.1(ENSG00000291175):​n.134+6250G>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 (2175 hom., cov: 52)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000291175 ENST00000686949.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• 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=-1.02).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291175	ENST00000686949.1		n.134+6250G>T		intron	N/A
	ENSG00000291175	ENST00000701132.2		n.134+6250G>T		intron	N/A
	ENSG00000291175	ENST00000717223.1		n.560+7380G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65184 AN: 150980 Hom.: 2177 Cov.: 52

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.468

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: 0.431 AC: 65196 AN: 151096 Hom.: 2175 Cov.: 52 AF XY: 0.428 AC XY: 31600 AN XY: 73868

African (AFR) AF: 0.319 AC: 13069 AN: 41016

American (AMR) AF: 0.442 AC: 6686 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1758 AN: 3464

East Asian (EAS) AF: 0.315 AC: 1616 AN: 5128

South Asian (SAS) AF: 0.467 AC: 2241 AN: 4796

European-Finnish (FIN) AF: 0.428 AC: 4490 AN: 10502

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

European-Non Finnish (NFE) AF: 0.498 AC: 33739 AN: 67746

Other (OTH) AF: 0.468 AC: 982 AN: 2100

Alfa AF: 0.455 Hom.: 300

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.16
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs2693371; hg19: chr17-43655688; COSMIC: COSV69471729;