rs7882574

Variant names:

• chrX-11687501-A-C
• rs7882574
• ENST00000634846.1:n.1104-18311T>G

Variant summary

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

The ENST00000634846.1(MSL3-DT):​n.1104-18311T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 109,012 control chromosomes in the GnomAD database, including 1,895 homozygotes. There are 4,889 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 0.16 (1895 hom., 4889 hem., cov: 21)
• Consequence: MSL3-DT ENST00000634846.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 0 publications found

Genes affected

MSL3-DT (HGNC:56856): (MSL3 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634846.1. 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
	MSL3-DT	ENST00000634846.1	TSL:5	n.1104-18311T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.164 AC: 17860 AN: 108959 Hom.: 1887 Cov.: 21

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.0147

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.0962

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.0544

Gnomad MID AF: 0.0944

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.164 AC: 17912 AN: 109012 Hom.: 1895 Cov.: 21 AF XY: 0.156 AC XY: 4889 AN XY: 31430

African (AFR) AF: 0.364 AC: 10828 AN: 29748

American (AMR) AF: 0.233 AC: 2378 AN: 10201

Ashkenazi Jewish (ASJ) AF: 0.0962 AC: 252 AN: 2619

East Asian (EAS) AF: 0.233 AC: 797 AN: 3427

South Asian (SAS) AF: 0.0826 AC: 202 AN: 2447

European-Finnish (FIN) AF: 0.0544 AC: 314 AN: 5772

Middle Eastern (MID) AF: 0.0943 AC: 20 AN: 212

European-Non Finnish (NFE) AF: 0.0549 AC: 2881 AN: 52434

Other (OTH) AF: 0.156 AC: 230 AN: 1472

Alfa AF: 0.106 Hom.: 5144

Bravo AF: 0.193

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.7
DANN	Benign	0.59
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs7882574; hg19: chrX-11705621;