rs5981086

Positions:

• chrX-71189260-G-A

Variant summary

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

The ENST00000664514.3(ENSG00000228427):​n.332-5243C>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 0.138 in 110,271 control chromosomes in the GnomAD database, including 1,197 homozygotes. There are 4,183 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 (1197 hom., 4183 hem., cov: 21)
• Consequence: ENST00000664514.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985688	XR_001755878.2	n.286-5243C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000664514.3	n.332-5243C>T		intron_variant, non_coding_transcript_variant
	ENST00000450860.1	n.268-5243C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000652147.2	n.322-5247C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.138 AC: 15178 AN: 110218 Hom.: 1192 Cov.: 21 AF XY: 0.128 AC XY: 4179 AN XY: 32552

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0909

Gnomad SAS AF: 0.0570

Gnomad FIN AF: 0.0840

Gnomad MID AF: 0.0979

Gnomad NFE AF: 0.0719

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.138 AC: 15194 AN: 110271 Hom.: 1197 Cov.: 21 AF XY: 0.128 AC XY: 4183 AN XY: 32615

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.0911

Gnomad4 SAS AF: 0.0549

Gnomad4 FIN AF: 0.0840

Gnomad4 NFE AF: 0.0719

Gnomad4 OTH AF: 0.120

Alfa AF: 0.107 Hom.: 583

Bravo AF: 0.148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.55
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5981086; hg19: chrX-70409110;