chrX-8439288-C-A

Position:

• chrX-8439288-C-A

Variant summary

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

The XR_001755783.2(LOC107985675):​n.6226-540C>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 0.271 in 109,562 control chromosomes in the GnomAD database, including 3,018 homozygotes. There are 8,256 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 0.27 (3018 hom., 8256 hem., cov: 22)
• Consequence: LOC107985675 XR_001755783.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241

Genes affected

LOC107985675 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985675	XR_001755783.2	n.6226-540C>A		intron_variant, non_coding_transcript_variant
LOC107985675	XR_001755782.2	n.1986-540C>A		intron_variant, non_coding_transcript_variant
LOC107985675	XR_001755784.2	n.1986-540C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.271 AC: 29731 AN: 109513 Hom.: 3020 Cov.: 22 AF XY: 0.259 AC XY: 8248 AN XY: 31799

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.271 AC: 29731 AN: 109562 Hom.: 3018 Cov.: 22 AF XY: 0.259 AC XY: 8256 AN XY: 31858

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.289

Alfa AF: 0.259 Hom.: 5368

Bravo AF: 0.281

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521594; hg19: chrX-8407329;