X-112871491-T-C

Variant names:

• chrX-112871491-T-C
• rs763299
• ENST00000738665.1:n.277+24412T>C

Variant summary

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

The ENST00000738665.1(ENSG00000286072):​n.277+24412T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 111,221 control chromosomes in the GnomAD database, including 1,138 homozygotes. There are 3,184 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 0.10 (1138 hom., 3184 hem., cov: 22)
• Consequence: ENSG00000286072 ENST00000738665.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 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+24412T>C		intron	N/A
	ENSG00000286072	ENST00000738666.1		n.396+24412T>C		intron	N/A
	ENSG00000286072	ENST00000738667.1		n.410+24412T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.104 AC: 11617 AN: 111173 Hom.: 1138 Cov.: 22

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0136

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.0713

Gnomad FIN AF: 0.00116

Gnomad MID AF: 0.0460

Gnomad NFE AF: 0.00427

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.105 AC: 11645 AN: 111221 Hom.: 1138 Cov.: 22 AF XY: 0.0952 AC XY: 3184 AN XY: 33443

African (AFR) AF: 0.288 AC: 8746 AN: 30404

American (AMR) AF: 0.154 AC: 1608 AN: 10455

Ashkenazi Jewish (ASJ) AF: 0.0136 AC: 36 AN: 2639

East Asian (EAS) AF: 0.190 AC: 668 AN: 3509

South Asian (SAS) AF: 0.0712 AC: 188 AN: 2639

European-Finnish (FIN) AF: 0.00116 AC: 7 AN: 6029

Middle Eastern (MID) AF: 0.0461 AC: 10 AN: 217

European-Non Finnish (NFE) AF: 0.00427 AC: 227 AN: 53119

Other (OTH) AF: 0.102 AC: 155 AN: 1524

Alfa AF: 0.0595 Hom.: 299

Bravo AF: 0.126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.9
DANN	Benign	0.69
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs763299; hg19: chrX-112114719;