ENST00000412173.1:n.451C>T

Variant names:

• chrX-142148416-G-A
• rs5908188
• ENST00000412173.1:n.451C>T

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000236205 ENST00000412173.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.942
• Publications: 0 publications found

Genes affected

ENSG00000236205 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412173.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000236205	ENST00000412173.1	TSL:6	n.451C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000288098	ENST00000664519.1		n.223-47291G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.139 AC: 15366 AN: 110322 Hom.: 770 Cov.: 21

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 7

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.132 AC: 4012 AN: 30298

American (AMR) AF: 0.155 AC: 1612 AN: 10417

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 452 AN: 2627

East Asian (EAS) AF: 0.0126 AC: 44 AN: 3481

South Asian (SAS) AF: 0.184 AC: 466 AN: 2531

European-Finnish (FIN) AF: 0.197 AC: 1154 AN: 5844

Middle Eastern (MID) AF: 0.179 AC: 38 AN: 212

European-Non Finnish (NFE) AF: 0.139 AC: 7355 AN: 52800

Other (OTH) AF: 0.142 AC: 211 AN: 1487

Alfa AF: 0.142 Hom.: 2353

Bravo AF: 0.136

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.4
DANN	Benign	0.89
PhyloP100		0.94

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5908188;

hg19: chrX-141236202;