rs201647

Positions:

• chrX-127248230-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.723+312G>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 0.0303 in 111,594 control chromosomes in the GnomAD database, including 92 homozygotes. There are 973 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 0.030 (92 hom., 973 hem., cov: 23)
• Consequence: LOC107985709 XR_007068367.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

LOC107985709 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.086 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985709	XR_007068367.1	n.723+312G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0302 AC: 3367 AN: 111542 Hom.: 93 Cov.: 23 AF XY: 0.0285 AC XY: 961 AN XY: 33748

Gnomad AFR AF: 0.0885

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.0234

Gnomad ASJ AF: 0.0212

Gnomad EAS AF: 0.00197

Gnomad SAS AF: 0.0442

Gnomad FIN AF: 0.000167

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00311

Gnomad OTH AF: 0.0341

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

GnomAD4 genome AF: 0.0303 AC: 3378 AN: 111594 Hom.: 92 Cov.: 23 AF XY: 0.0288 AC XY: 973 AN XY: 33810

Gnomad4 AFR AF: 0.0888

Gnomad4 AMR AF: 0.0233

Gnomad4 ASJ AF: 0.0212

Gnomad4 EAS AF: 0.00197

Gnomad4 SAS AF: 0.0440

Gnomad4 FIN AF: 0.000167

Gnomad4 NFE AF: 0.00309

Gnomad4 OTH AF: 0.0337

Alfa AF: 0.0209 Hom.: 94

Bravo AF: 0.0369

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.047
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs201647; hg19: chrX-126382213;