rs3116911

chrX-113075146-G-AchrX-113075146-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NR_110399.2(LOC101928437):n.115+2028G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.66 (17520 hom., 21099 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: LOC101928437 NR_110399.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.573

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS2: High Homozygotes in GnomAd at 17516 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928437	NR_110399.2	n.115+2028G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651919.1	n.346+2028G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.660 AC: 72323 AN: 109640 Hom.: 17516 Cov.: 23 AF XY: 0.657 AC XY: 21058 AN XY: 32044

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.648

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.660 AC: 72368 AN: 109691 Hom.: 17520 Cov.: 23 AF XY: 0.657 AC XY: 21099 AN XY: 32103

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.640

Alfa AF: 0.626 Hom.: 4885

Bravo AF: 0.678

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.71
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3116911; hg19: chrX-112318374;