rs3116911

Variant names:

• chrX-113075146-G-A
• rs3116911
• ENST00000651919.1:n.346+2028G>A

Your query was ambiguous. Multiple possible variants found:

• chrX-113075146-G-A
• chrX-113075146-G-C

Variant summary

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

The NR_110399.2(LOC101928437):​n.115+2028G>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 0.66 (17520 hom., 21099 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: LOC101928437 NR_110399.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.573
• Publications: 2 publications found

Genes affected

ENSG00000286072 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_110399.2. 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
	LOC101928437	NR_110399.2		n.115+2028G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286072	ENST00000651919.1		n.346+2028G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.660 AC: 72323 AN: 109640 Hom.: 17516 Cov.: 23

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.648

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: 0.660 AC: 72368 AN: 109691 Hom.: 17520 Cov.: 23 AF XY: 0.657 AC XY: 21099 AN XY: 32103

African (AFR) AF: 0.835 AC: 25365 AN: 30370

American (AMR) AF: 0.680 AC: 6961 AN: 10231

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 1733 AN: 2611

East Asian (EAS) AF: 0.517 AC: 1793 AN: 3468

South Asian (SAS) AF: 0.622 AC: 1618 AN: 2602

European-Finnish (FIN) AF: 0.545 AC: 3092 AN: 5677

Middle Eastern (MID) AF: 0.635 AC: 132 AN: 208

European-Non Finnish (NFE) AF: 0.579 AC: 30323 AN: 52374

Other (OTH) AF: 0.640 AC: 951 AN: 1485

Alfa AF: 0.626 Hom.: 4885

Bravo AF: 0.678

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.41
PhyloP100		0.57

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: rs3116911;

hg19: chrX-112318374;