X-28585448-T-C

Variant names:

• chrX-28585448-T-C
• rs1349846
• ENST00000456037.1:n.88+860A>G

Variant summary

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

The ENST00000456037.1(ENSG00000223742):​n.88+860A>G 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 0.64 (17047 hom., 19999 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000223742 ENST00000456037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.994
• Publications: 4 publications found

Genes affected

ENSG00000223742 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456037.1. 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
	ENSG00000223742	ENST00000456037.1	TSL:5	n.88+860A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.639 AC: 70217 AN: 109810 Hom.: 17044 Cov.: 22

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.520

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.612

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: 0.640 AC: 70259 AN: 109861 Hom.: 17047 Cov.: 22 AF XY: 0.623 AC XY: 19999 AN XY: 32119

African (AFR) AF: 0.852 AC: 25725 AN: 30178

American (AMR) AF: 0.614 AC: 6299 AN: 10251

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1399 AN: 2626

East Asian (EAS) AF: 0.669 AC: 2302 AN: 3439

South Asian (SAS) AF: 0.433 AC: 1111 AN: 2566

European-Finnish (FIN) AF: 0.513 AC: 2938 AN: 5727

Middle Eastern (MID) AF: 0.529 AC: 110 AN: 208

European-Non Finnish (NFE) AF: 0.553 AC: 29151 AN: 52698

Other (OTH) AF: 0.604 AC: 909 AN: 1504

Alfa AF: 0.587 Hom.: 25190

Bravo AF: 0.663

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
DANN	Benign	0.71
PhyloP100		-0.99

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: rs1349846;

hg19: chrX-28603565;