rs7885872

Variant names:

• chrX-142490379-A-G
• rs7885872
• ENST00000664519.1:n.443-56002A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664519.1(ENSG00000288098):​n.443-56002A>G variant causes a intron 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: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 1 publications found

Genes affected

ENSG00000288098 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664519.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288098	ENST00000664519.1		n.443-56002A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0828 AC: 9203 AN: 111081 Hom.: 583 Cov.: 22

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

African (AFR) AF: 0.204 AC: 6216 AN: 30451

American (AMR) AF: 0.0636 AC: 668 AN: 10507

Ashkenazi Jewish (ASJ) AF: 0.0151 AC: 40 AN: 2645

East Asian (EAS) AF: 0.201 AC: 694 AN: 3457

South Asian (SAS) AF: 0.115 AC: 302 AN: 2615

European-Finnish (FIN) AF: 0.0178 AC: 107 AN: 6026

Middle Eastern (MID) AF: 0.0648 AC: 14 AN: 216

European-Non Finnish (NFE) AF: 0.0194 AC: 1031 AN: 53028

Other (OTH) AF: 0.0901 AC: 136 AN: 1509

Alfa AF: 0.0517 Hom.: 769

Bravo AF: 0.0946

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.54
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs7885872; hg19: chrX-141578165;