rs7885872

chrX-142490379-A-G

Variant summary

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

The ENST00000664519.1(ENSG00000288098):n.443-56002A>G 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 0.0831 in 111,136 control chromosomes in the GnomAD database, including 582 homozygotes. There are 2,602 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 0.083 (582 hom., 2602 hem., cov: 22)
• Consequence: ENST00000664519.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 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
	ENST00000664519.1	n.443-56002A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0828 AC: 9203 AN: 111081 Hom.: 583 Cov.: 22 AF XY: 0.0772 AC XY: 2575 AN XY: 33369

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0323

Gnomad AMR AF: 0.0636

Gnomad ASJ AF: 0.0151

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0178

Gnomad MID AF: 0.0591

Gnomad NFE AF: 0.0194

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.0831 AC: 9230 AN: 111136 Hom.: 582 Cov.: 22 AF XY: 0.0778 AC XY: 2602 AN XY: 33434

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.0636

Gnomad4 ASJ AF: 0.0151

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0178

Gnomad4 NFE AF: 0.0194

Gnomad4 OTH AF: 0.0901

Alfa AF: 0.0509 Hom.: 664

Bravo AF: 0.0946

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.0
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7885872; hg19: chrX-141578165;