rs2463520

Variant names:

• chr17-45581989-C-A
• rs2463520
• ENST00000686949.1:n.134+2583G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-45581989-C-A
• chr17-45581989-C-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+2583G>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 (2209 hom., cov: 56)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000291175 ENST00000686949.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216
• 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=-0.97).

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+2583G>T		intron	N/A
	ENSG00000291175	ENST00000701132.2		n.134+2583G>T		intron	N/A
	ENSG00000291175	ENST00000717223.1		n.560+3713G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65693 AN: 150980 Hom.: 2211 Cov.: 56

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.470

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: 0.435 AC: 65705 AN: 151096 Hom.: 2209 Cov.: 56 AF XY: 0.431 AC XY: 31835 AN XY: 73848

African (AFR) AF: 0.327 AC: 13440 AN: 41050

American (AMR) AF: 0.447 AC: 6787 AN: 15174

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

East Asian (EAS) AF: 0.317 AC: 1620 AN: 5114

South Asian (SAS) AF: 0.469 AC: 2252 AN: 4800

European-Finnish (FIN) AF: 0.429 AC: 4482 AN: 10456

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33767 AN: 67738

Other (OTH) AF: 0.469 AC: 985 AN: 2098

Alfa AF: 0.351 Hom.: 73

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.33
PhyloP100		-0.22

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: rs2463520;

hg19: chr17-43659355;