rs993010

chrX-34073562-T-C

Variant summary

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

The ENST00000668394.1(ENSG00000233928):n.392-2904T>C 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 0.56 (12865 hom., 17902 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENST00000668394.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd at 12871 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373153	XR_950542.4	n.372-2904T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668394.1	n.392-2904T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.560 AC: 61633 AN: 110141 Hom.: 12871 Cov.: 22 AF XY: 0.551 AC XY: 17885 AN XY: 32469

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.645

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.571

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: 0.559 AC: 61631 AN: 110194 Hom.: 12865 Cov.: 22 AF XY: 0.550 AC XY: 17902 AN XY: 32532

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.570

Alfa AF: 0.633 Hom.: 69151

Bravo AF: 0.542

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.8
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs993010; hg19: chrX-34091679;