rs5931921

chrX-127293968-C-T

Variant summary

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

The XR_007068367.1(LOC107985709):n.187+89G>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 0.216 in 109,352 control chromosomes in the GnomAD database, including 2,053 homozygotes. There are 6,794 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 0.22 (2053 hom., 6794 hem., cov: 21)
• Consequence: LOC107985709 XR_007068367.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.610

Genes affected

LOC107985709 (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 = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985709	XR_007068367.1	n.187+89G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.216 AC: 23583 AN: 109303 Hom.: 2052 Cov.: 21 AF XY: 0.213 AC XY: 6781 AN XY: 31879

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0236

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.216 AC: 23588 AN: 109352 Hom.: 2053 Cov.: 21 AF XY: 0.213 AC XY: 6794 AN XY: 31938

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.0234

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.211

Alfa AF: 0.232 Hom.: 4696

Bravo AF: 0.220

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.5
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: rs5931921; hg19: chrX-126427951;