X-112864896-A-G

Variant names:

• chrX-112864896-A-G
• rs648170
• ENST00000738665.1:n.277+17817A>G

Variant summary

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

The ENST00000738665.1(ENSG00000286072):​n.277+17817A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 110,314 control chromosomes in the GnomAD database, including 6,741 homozygotes. There are 11,655 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 0.37 (6741 hom., 11655 hem., cov: 22)
• Consequence: ENSG00000286072 ENST00000738665.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221
• Publications: 2 publications found

Genes affected

ENSG00000286072 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000738665.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286072	ENST00000738665.1		n.277+17817A>G		intron	N/A
	ENSG00000286072	ENST00000738666.1		n.396+17817A>G		intron	N/A
	ENSG00000286072	ENST00000738667.1		n.410+17817A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.369 AC: 40737 AN: 110258 Hom.: 6736 Cov.: 22

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.370 AC: 40773 AN: 110314 Hom.: 6741 Cov.: 22 AF XY: 0.358 AC XY: 11655 AN XY: 32600

African (AFR) AF: 0.601 AC: 18179 AN: 30241

American (AMR) AF: 0.478 AC: 4937 AN: 10332

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 371 AN: 2628

East Asian (EAS) AF: 0.580 AC: 2005 AN: 3459

South Asian (SAS) AF: 0.183 AC: 477 AN: 2600

European-Finnish (FIN) AF: 0.303 AC: 1778 AN: 5866

Middle Eastern (MID) AF: 0.238 AC: 51 AN: 214

European-Non Finnish (NFE) AF: 0.233 AC: 12291 AN: 52809

Other (OTH) AF: 0.369 AC: 553 AN: 1498

Alfa AF: 0.305 Hom.: 2180

Bravo AF: 0.403

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.42
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs648170; hg19: chrX-112108124;