chrX-142148416-G-A

Position:

• chrX-142148416-G-A

Variant summary

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

The ENST00000412173.1(ENSG00000236205):​n.451C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 110,377 control chromosomes in the GnomAD database, including 770 homozygotes. There are 4,493 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 0.14 (770 hom., 4493 hem., cov: 21)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000412173.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.942

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000412173.1	n.451C>T		non_coding_transcript_exon_variant	1/1
	ENST00000664519.1	n.223-47291G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.139 AC: 15366 AN: 110322 Hom.: 770 Cov.: 21 AF XY: 0.137 AC XY: 4482 AN XY: 32616

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0412

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0126

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.145

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.139 AC: 15372 AN: 110377 Hom.: 770 Cov.: 21 AF XY: 0.137 AC XY: 4493 AN XY: 32681

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.0126

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.142

Alfa AF: 0.143 Hom.: 2161

Bravo AF: 0.136

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.4
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5908188; hg19: chrX-141236202;