chrX-142148416-G-A

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100533669		n.142148416G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000236205	ENST00000412173.1	n.451C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000288098	ENST00000664519.1	n.223-47291G>A		intron_variant	Intron 1 of 9

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 v4.3

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

Other links and lift over

dbSNP: rs5908188; hg19: chrX-141236202;