rs6527664

Variant names:

• chrX-16156434-A-G
• rs6527664
• ENST00000422438.5:n.77+1319T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000422438.5(MAGEB17-AS1):​n.77+1319T>C variant causes a intron 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 ENST00000422438.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MAGEB17-AS1	NR_187144.1	n.1623+1319T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAGEB17-AS1	ENST00000422438.5	n.77+1319T>C		intron_variant	Intron 1 of 3	3
MAGEB17-AS1	ENST00000435789.1	n.710+1319T>C		intron_variant	Intron 4 of 5	5
MAGEB17-AS1	ENST00000454712.8	n.620+1319T>C		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.426 AC: 47076 AN: 110385 Hom.: 8331 Cov.: 22

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

African (AFR) AF: 0.652 AC: 19670 AN: 30185

American (AMR) AF: 0.401 AC: 4178 AN: 10430

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 947 AN: 2629

East Asian (EAS) AF: 0.166 AC: 585 AN: 3520

South Asian (SAS) AF: 0.227 AC: 591 AN: 2607

European-Finnish (FIN) AF: 0.241 AC: 1425 AN: 5905

Middle Eastern (MID) AF: 0.360 AC: 76 AN: 211

European-Non Finnish (NFE) AF: 0.356 AC: 18776 AN: 52775

Other (OTH) AF: 0.390 AC: 588 AN: 1509

Alfa AF: 0.391 Hom.: 17736

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
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs6527664; hg19: chrX-16174557;