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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449111.5. 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
	EOLA2-DT	ENST00000449111.5	TSL:5	n.2831-120955T>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6649480;

hg19: chrX-149270442;