X-152160285-C-T

Variant summary

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

The ENST00000453915.1(ENSG00000231937):n.110-3912C>T 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 0.324 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: ENST00000453915.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000453915.1	n.110-3912C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.324 AC: 35370 AN: 109304 Hom.: 4688 Cov.: 22 AF XY: 0.308 AC XY: 9774 AN XY: 31684

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

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.316

Alfa AF: 0.253 Hom.: 17704

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11094547; hg19: chrX-151328757;