rs2353576

Variant names:

• chrX-16153837-A-C
• rs2353576
• ENST00000422438.5:n.161-374T>G

Your query was ambiguous. Multiple possible variants found:

• chrX-16153837-A-C
• chrX-16153837-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000422438.5(ENSG00000238178):​n.161-374T>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 (16237 hom., 20551 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000238178 ENST00000422438.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

Genes affected

ENSG00000238178 (HGNC:56739): (MAGEB17 antisense RNA 1)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGEB17-AS1	NR_187144.1	n.1707-374T>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000238178	ENST00000422438.5	n.161-374T>G		intron_variant	Intron 2 of 3	3
ENSG00000238178	ENST00000435789.1	n.794-374T>G		intron_variant	Intron 5 of 5	5
ENSG00000238178	ENST00000454712.7	n.631-374T>G		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.636 AC: 70234 AN: 110365 Hom.: 16234 Cov.: 22 AF XY: 0.628 AC XY: 20498 AN XY: 32631

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.613

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: 0.636 AC: 70279 AN: 110418 Hom.: 16237 Cov.: 22 AF XY: 0.629 AC XY: 20551 AN XY: 32694

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.612

Alfa AF: 0.568 Hom.: 34127

Bravo AF: 0.653

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2353576; hg19: chrX-16171960;