X-43427013-T-C

Position:

• chrX-43427013-T-C

Variant summary

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

The ENST00000649774.1(ENSG00000285899):​n.619-11322T>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 0.0209 in 111,952 control chromosomes in the GnomAD database, including 41 homozygotes. There are 691 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 0.021 (41 hom., 691 hem., cov: 23)
• Consequence: ENST00000649774.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.066 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649774.1	n.619-11322T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0209 AC: 2335 AN: 111895 Hom.: 40 Cov.: 23 AF XY: 0.0202 AC XY: 689 AN XY: 34053

Gnomad AFR AF: 0.00426

Gnomad AMI AF: 0.00291

Gnomad AMR AF: 0.0699

Gnomad ASJ AF: 0.0238

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00862

Gnomad FIN AF: 0.0307

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0217

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0209 AC: 2340 AN: 111952 Hom.: 41 Cov.: 23 AF XY: 0.0203 AC XY: 691 AN XY: 34120

Gnomad4 AFR AF: 0.00425

Gnomad4 AMR AF: 0.0702

Gnomad4 ASJ AF: 0.0238

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00901

Gnomad4 FIN AF: 0.0307

Gnomad4 NFE AF: 0.0217

Gnomad4 OTH AF: 0.0236

Alfa AF: 0.0241 Hom.: 203

Bravo AF: 0.0251

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521430; hg19: chrX-43286262;