rs6649480

Variant names:

• chrX-150102211-T-A
• rs6649480
• ENST00000449111.5:n.2831-120955T>A

Your query was ambiguous. Multiple possible variants found:

• chrX-150102211-T-A
• chrX-150102211-T-C
• chrX-150102211-T-G

Variant summary

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

The ENST00000449111.5(EOLA2-DT):​n.2831-120955T>A 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 0.97 (36841 hom., 31617 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: EOLA2-DT ENST00000449111.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 1 publications found

Genes affected

EOLA2-DT (HGNC:48579): (EOLA2 divergent transcript)

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
EOLA2-DT	ENST00000449111.5	n.2831-120955T>A		intron_variant	Intron 11 of 14	5

Frequencies

GnomAD3 genomes AF: 0.974 AC: 107230 AN: 110127 Hom.: 36849 Cov.: 22

Gnomad AFR AF: 0.909

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.991

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.992

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.982

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: 0.974 AC: 107273 AN: 110181 Hom.: 36841 Cov.: 22 AF XY: 0.976 AC XY: 31617 AN XY: 32385

African (AFR) AF: 0.908 AC: 27493 AN: 30263

American (AMR) AF: 0.991 AC: 10265 AN: 10357

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2630 AN: 2630

East Asian (EAS) AF: 1.00 AC: 3477 AN: 3477

South Asian (SAS) AF: 1.00 AC: 2503 AN: 2504

European-Finnish (FIN) AF: 1.00 AC: 5801 AN: 5801

Middle Eastern (MID) AF: 0.991 AC: 213 AN: 215

European-Non Finnish (NFE) AF: 1.00 AC: 52754 AN: 52771

Other (OTH) AF: 0.982 AC: 1459 AN: 1485

Alfa AF: 0.978 Hom.: 3322

Bravo AF: 0.969

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.63
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs6649480; hg19: chrX-149270442;