X-113118620-T-C

Position:

• chrX-113118620-T-C

Variant summary

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

The NR_110399.2(LOC101928437):​n.231+6555T>C 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 0.352 in 111,008 control chromosomes in the GnomAD database, including 5,336 homozygotes. There are 11,418 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 0.35 (5336 hom., 11418 hem., cov: 23)
• Consequence: LOC101928437 NR_110399.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928437	NR_110399.2	n.231+6555T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651919.1	n.346+45502T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.352 AC: 39034 AN: 110958 Hom.: 5340 Cov.: 23 AF XY: 0.344 AC XY: 11402 AN XY: 33192

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.375

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.352 AC: 39045 AN: 111008 Hom.: 5336 Cov.: 23 AF XY: 0.343 AC XY: 11418 AN XY: 33252

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.342

Alfa AF: 0.371 Hom.: 2444

Bravo AF: 0.339

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12164331; hg19: chrX-112361848;