rs1972809

Variant names:

• chrX-120733621-A-G
• rs1972809

Variant summary

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

The variant allele was found at a frequency of 0.467 in 110,620 control chromosomes in the GnomAD database, including 9,038 homozygotes. There are 15,084 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 0.47 (9038 hom., 15084 hem., cov: 22)
• Consequence: GLRX5P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338
• Publications: 4 publications found

Genes affected

GLRX5P1 (HGNC:55062): (GLRX5 pseudogene 1)

ENSG00000293858 (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 = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLRX5P1		n.120733621A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293858	ENST00000719513.1	n.247+19018T>C		intron_variant	Intron 1 of 2
ENSG00000293858	ENST00000719514.1	n.138+19018T>C		intron_variant	Intron 1 of 1
ENSG00000293858	ENST00000719515.1	n.273-3600T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.467 AC: 51644 AN: 110566 Hom.: 9040 Cov.: 22

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.460

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.467 AC: 51687 AN: 110620 Hom.: 9038 Cov.: 22 AF XY: 0.459 AC XY: 15084 AN XY: 32874

African (AFR) AF: 0.610 AC: 18476 AN: 30296

American (AMR) AF: 0.455 AC: 4758 AN: 10447

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1035 AN: 2637

East Asian (EAS) AF: 0.440 AC: 1541 AN: 3502

South Asian (SAS) AF: 0.396 AC: 1048 AN: 2646

European-Finnish (FIN) AF: 0.408 AC: 2360 AN: 5788

Middle Eastern (MID) AF: 0.475 AC: 103 AN: 217

European-Non Finnish (NFE) AF: 0.402 AC: 21290 AN: 52921

Other (OTH) AF: 0.459 AC: 688 AN: 1499

Alfa AF: 0.448 Hom.: 3486

Bravo AF: 0.481

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.52
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs1972809; hg19: chrX-119867475; COSMIC: COSV70204342;