X-71187240-C-T

Variant summary

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

The ENST00000664514.3(ENSG00000228427):n.332-3223G>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 0.485 in 110,134 control chromosomes in the GnomAD database, including 9,780 homozygotes. There are 15,644 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 0.49 (9780 hom., 15644 hem., cov: 22)
• Consequence: ENST00000664514.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985688	XR_001755878.2	n.286-3223G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664514.3	n.332-3223G>A		intron_variant, non_coding_transcript_variant
	ENST00000450860.1	n.268-3223G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000652147.2	n.322-3227G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.485 AC: 53392 AN: 110081 Hom.: 9772 Cov.: 22 AF XY: 0.482 AC XY: 15602 AN XY: 32347

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.485 AC: 53443 AN: 110134 Hom.: 9780 Cov.: 22 AF XY: 0.483 AC XY: 15644 AN XY: 32410

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.540

Alfa AF: 0.433 Hom.: 3794

Bravo AF: 0.509

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.1
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6624539; hg19: chrX-70407090;