X-8391136-T-C

Position:

• chrX-8391136-T-C

Variant summary

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

The XR_001755782.2(LOC107985675):​n.1986-48692T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 110,728 control chromosomes in the GnomAD database, including 3,579 homozygotes. There are 9,524 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 0.29 (3579 hom., 9524 hem., cov: 22)
• Consequence: LOC107985675 XR_001755782.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

Genes affected

LOC107985675 (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 (EAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985675	XR_001755782.2	n.1986-48692T>C		intron_variant
LOC107985675	XR_001755783.2	n.1986-29951T>C		intron_variant
LOC107985675	XR_001755784.2	n.1986-48692T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.294 AC: 32537 AN: 110676 Hom.: 3579 Cov.: 22 AF XY: 0.289 AC XY: 9504 AN XY: 32930

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.294 AC: 32556 AN: 110728 Hom.: 3579 Cov.: 22 AF XY: 0.289 AC XY: 9524 AN XY: 32990

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.285

Alfa AF: 0.267 Hom.: 14656

Bravo AF: 0.298

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1534255; hg19: chrX-8359177;