X-16156434-A-G

Position:

• chrX-16156434-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435789.1(MAGEB17-AS1):​n.710+1319T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 110,439 control chromosomes in the GnomAD database, including 8,334 homozygotes. There are 13,169 hemizygotes in GnomAD. 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 0.43 (8334 hom., 13169 hem., cov: 22)
• Consequence: MAGEB17-AS1 ENST00000435789.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318

Genes affected

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

LOC128966703 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC128966703	XR_008485585.1	n.1623+1319T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAGEB17-AS1	ENST00000435789.1	n.710+1319T>C		intron_variant, non_coding_transcript_variant		5
MAGEB17-AS1	ENST00000422438.5	n.77+1319T>C		intron_variant, non_coding_transcript_variant		3
MAGEB17-AS1	ENST00000454712.7	n.547+1319T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.426 AC: 47076 AN: 110385 Hom.: 8331 Cov.: 22 AF XY: 0.401 AC XY: 13123 AN XY: 32703

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.353

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.393

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.427 AC: 47121 AN: 110439 Hom.: 8334 Cov.: 22 AF XY: 0.402 AC XY: 13169 AN XY: 32767

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.390

Alfa AF: 0.379 Hom.: 12557

Bravo AF: 0.450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6527664; hg19: chrX-16174557;