rs7059886

Variant names:

• chrX-3492628-A-G
• rs7059886
• ENST00000811167.1:n.174+27689T>C

Variant summary

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

The ENST00000811167.1(ENSG00000305467):​n.174+27689T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 110,636 control chromosomes in the GnomAD database, including 2,135 homozygotes. There are 6,858 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 0.21 (2135 hom., 6858 hem., cov: 22)
• Consequence: ENSG00000305467 ENST00000811167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 2 publications found

Genes affected

ENSG00000305467 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305467	ENST00000811167.1	n.174+27689T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.215 AC: 23747 AN: 110582 Hom.: 2135 Cov.: 22

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.314

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.215 AC: 23753 AN: 110636 Hom.: 2135 Cov.: 22 AF XY: 0.209 AC XY: 6858 AN XY: 32888

African (AFR) AF: 0.0906 AC: 2775 AN: 30614

American (AMR) AF: 0.190 AC: 1966 AN: 10371

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 781 AN: 2639

East Asian (EAS) AF: 0.201 AC: 698 AN: 3477

South Asian (SAS) AF: 0.307 AC: 776 AN: 2529

European-Finnish (FIN) AF: 0.267 AC: 1557 AN: 5834

Middle Eastern (MID) AF: 0.319 AC: 69 AN: 216

European-Non Finnish (NFE) AF: 0.278 AC: 14644 AN: 52764

Other (OTH) AF: 0.228 AC: 345 AN: 1514

Alfa AF: 0.220 Hom.: 1952

Bravo AF: 0.205

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.34
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs7059886; hg19: chrX-3410669;