rs5929554

chrX-113089796-T-A

Variant summary

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

The NR_110399.2(LOC101928437):n.115+16678T>A 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 0.412 in 110,002 control chromosomes in the GnomAD database, including 7,160 homozygotes. There are 13,176 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 0.41 (7160 hom., 13176 hem., cov: 22)
• Consequence: LOC101928437 NR_110399.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928437	NR_110399.2	n.115+16678T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651919.1	n.346+16678T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.412 AC: 45333 AN: 109951 Hom.: 7165 Cov.: 22 AF XY: 0.408 AC XY: 13166 AN XY: 32267

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.410

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.412 AC: 45334 AN: 110002 Hom.: 7160 Cov.: 22 AF XY: 0.408 AC XY: 13176 AN XY: 32328

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.415

Alfa AF: 0.457 Hom.: 3223

Bravo AF: 0.401

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.8
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5929554; hg19: chrX-112333024;