chrX-16153837-A-C

Variant names:

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

Variant summary

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

The ENST00000422438.5(MAGEB17-AS1):​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: MAGEB17-AS1 ENST00000422438.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422438.5. 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
	MAGEB17-AS1	NR_187144.1		n.1707-374T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGEB17-AS1	ENST00000422438.5	TSL:3	n.161-374T>G		intron	N/A
	MAGEB17-AS1	ENST00000435789.1	TSL:5	n.794-374T>G		intron	N/A
	MAGEB17-AS1	ENST00000454712.8	TSL:3	n.704-374T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.636 AC: 70234 AN: 110365 Hom.: 16234 Cov.: 22

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

African (AFR) AF: 0.778 AC: 23593 AN: 30317

American (AMR) AF: 0.629 AC: 6569 AN: 10446

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1431 AN: 2629

East Asian (EAS) AF: 0.697 AC: 2438 AN: 3496

South Asian (SAS) AF: 0.565 AC: 1476 AN: 2613

European-Finnish (FIN) AF: 0.547 AC: 3155 AN: 5768

Middle Eastern (MID) AF: 0.546 AC: 119 AN: 218

European-Non Finnish (NFE) AF: 0.573 AC: 30232 AN: 52767

Other (OTH) AF: 0.612 AC: 912 AN: 1490

Alfa AF: 0.591 Hom.: 55570

Bravo AF: 0.653

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.83
PhyloP100		1.2

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: rs2353576;

hg19: chrX-16171960;