X-16153837-A-C

Position:

• chrX-16153837-A-C

Variant summary

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

The ENST00000435789.1(MAGEB17-AS1):​n.794-374T>G variant causes a intron, non coding transcript 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: MAGEB17-AS1 ENST00000435789.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

Genes affected

MAGEB17-AS1 (HGNC:56739): (MAGEB17 antisense RNA 1)

LOC128966703 (HGNC:):

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/exons	MANE	UniProt
LOC128966703	XR_008485585.1	n.1707-374T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAGEB17-AS1	ENST00000435789.1	n.794-374T>G		intron_variant, non_coding_transcript_variant		5
MAGEB17-AS1	ENST00000422438.5	n.161-374T>G		intron_variant, non_coding_transcript_variant		3
MAGEB17-AS1	ENST00000454712.7	n.631-374T>G		intron_variant, non_coding_transcript_variant		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;