rs7051678

chrX-151534009-T-AchrX-151534009-T-C

Variant summary

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

The XR_938521.3(LOC105373367):n.229-1533A>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 0.108 in 111,872 control chromosomes in the GnomAD database, including 1,030 homozygotes. There are 3,306 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 0.11 (1030 hom., 3306 hem., cov: 23)
• Consequence: LOC105373367 XR_938521.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.933

Genes affected

LOC105373367 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373367	XR_938521.3	n.229-1533A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.108 AC: 12109 AN: 111821 Hom.: 1029 Cov.: 23 AF XY: 0.0968 AC XY: 3295 AN XY: 34029

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0397

Gnomad AMR AF: 0.0598

Gnomad ASJ AF: 0.0627

Gnomad EAS AF: 0.00927

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.0158

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0396

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.108 AC: 12121 AN: 111872 Hom.: 1030 Cov.: 23 AF XY: 0.0970 AC XY: 3306 AN XY: 34090

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.0597

Gnomad4 ASJ AF: 0.0627

Gnomad4 EAS AF: 0.00930

Gnomad4 SAS AF: 0.0454

Gnomad4 FIN AF: 0.0158

Gnomad4 NFE AF: 0.0395

Gnomad4 OTH AF: 0.105

Alfa AF: 0.00623 Hom.: 28

Bravo AF: 0.120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.9
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7051678; hg19: chrX-150702481;