rs7882595

Variant names:

• chrX-140531481-G-C
• rs7882595
• ENST00000797998.1:n.312+12637G>C

Variant summary

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

The ENST00000797998.1(ENSG00000303910):​n.312+12637G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 110,457 control chromosomes in the GnomAD database, including 3,287 homozygotes. There are 6,472 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 0.22 (3287 hom., 6472 hem., cov: 22)
• Consequence: ENSG00000303910 ENST00000797998.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 0 publications found

Genes affected

ENSG00000303910 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797998.1. 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
	ENSG00000303910	ENST00000797998.1		n.312+12637G>C		intron	N/A
	ENSG00000303910	ENST00000797999.1		n.392-1955G>C		intron	N/A
	ENSG00000303910	ENST00000798000.1		n.283-1955G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.218 AC: 24098 AN: 110405 Hom.: 3284 Cov.: 22

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.0969

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0842

Gnomad EAS AF: 0.0282

Gnomad SAS AF: 0.0488

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.219 AC: 24146 AN: 110457 Hom.: 3287 Cov.: 22 AF XY: 0.198 AC XY: 6472 AN XY: 32741

African (AFR) AF: 0.502 AC: 15136 AN: 30138

American (AMR) AF: 0.117 AC: 1218 AN: 10396

Ashkenazi Jewish (ASJ) AF: 0.0842 AC: 221 AN: 2624

East Asian (EAS) AF: 0.0283 AC: 99 AN: 3500

South Asian (SAS) AF: 0.0505 AC: 130 AN: 2575

European-Finnish (FIN) AF: 0.0837 AC: 498 AN: 5950

Middle Eastern (MID) AF: 0.129 AC: 28 AN: 217

European-Non Finnish (NFE) AF: 0.122 AC: 6439 AN: 52876

Other (OTH) AF: 0.207 AC: 311 AN: 1500

Alfa AF: 0.185 Hom.: 1114

Bravo AF: 0.237

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.33
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs7882595; hg19: chrX-139613646;