rs241389

Variant names:

• chrX-68868442-A-G
• rs241389
• ENST00000835181.1:n.93+6T>C

Variant summary

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

The ENST00000835181.1(ENSG00000308582):​n.93+6T>C variant causes a splice region, 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 0.63 (16247 hom., 19877 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000308582 ENST00000835181.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.616
• Publications: 1 publications found

Genes affected

ENSG00000308582 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835181.1. 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
	ENSG00000308582	ENST00000835181.1		n.93+6T>C		splice_region intron	N/A
	ENSG00000308582	ENST00000835182.1		n.-200T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.633 AC: 69561 AN: 109864 Hom.: 16252 Cov.: 22

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.675

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: 0.633 AC: 69605 AN: 109911 Hom.: 16247 Cov.: 22 AF XY: 0.617 AC XY: 19877 AN XY: 32239

African (AFR) AF: 0.751 AC: 22633 AN: 30119

American (AMR) AF: 0.587 AC: 6127 AN: 10443

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 1623 AN: 2613

East Asian (EAS) AF: 0.364 AC: 1247 AN: 3425

South Asian (SAS) AF: 0.417 AC: 1061 AN: 2543

European-Finnish (FIN) AF: 0.587 AC: 3376 AN: 5752

Middle Eastern (MID) AF: 0.679 AC: 144 AN: 212

European-Non Finnish (NFE) AF: 0.608 AC: 32006 AN: 52643

Other (OTH) AF: 0.667 AC: 998 AN: 1497

Alfa AF: 0.634 Hom.: 4923

Bravo AF: 0.635

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.57
DANN	Benign	0.42
PhyloP100		-0.62

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: rs241389;

hg19: chrX-68088285;