X-152160285-C-T

Variant names:

• chrX-152160285-C-T
• rs11094547
• ENST00000453915.1:n.110-3912C>T

Variant summary

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

The ENST00000453915.1(ENSG00000231937):​n.110-3912C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 109,361 control chromosomes in the GnomAD database, including 4,690 homozygotes. There are 9,816 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 0.32 (4690 hom., 9816 hem., cov: 22)
• Consequence: ENSG00000231937 ENST00000453915.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 1 publications found

Genes affected

ENSG00000231937 (HGNC:58378):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231937	ENST00000453915.1	n.110-3912C>T		intron_variant	Intron 2 of 3	5
ENSG00000231937	ENST00000778019.1	n.304-3912C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.324 AC: 35370 AN: 109304 Hom.: 4688 Cov.: 22

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.324 AC: 35408 AN: 109361 Hom.: 4690 Cov.: 22 AF XY: 0.309 AC XY: 9816 AN XY: 31751

African (AFR) AF: 0.494 AC: 14765 AN: 29880

American (AMR) AF: 0.336 AC: 3428 AN: 10188

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 376 AN: 2619

East Asian (EAS) AF: 0.149 AC: 515 AN: 3448

South Asian (SAS) AF: 0.348 AC: 864 AN: 2485

European-Finnish (FIN) AF: 0.222 AC: 1278 AN: 5756

Middle Eastern (MID) AF: 0.299 AC: 63 AN: 211

European-Non Finnish (NFE) AF: 0.254 AC: 13340 AN: 52618

Other (OTH) AF: 0.316 AC: 470 AN: 1485

Alfa AF: 0.277 Hom.: 27281

Bravo AF: 0.341

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.36
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs11094547; hg19: chrX-151328757;