rs5907306

Variant names:

• chrX-142508476-A-G
• rs5907306
• ENST00000664519.1:n.443-37905A>G

Variant summary

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

The ENST00000664519.1(ENSG00000288098):​n.443-37905A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 110,677 control chromosomes in the GnomAD database, including 7,283 homozygotes. There are 13,616 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 0.42 (7283 hom., 13616 hem., cov: 23)
• Consequence: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.838
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288098	ENST00000664519.1		n.443-37905A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.424 AC: 46883 AN: 110623 Hom.: 7274 Cov.: 23

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.424 AC: 46918 AN: 110677 Hom.: 7283 Cov.: 23 AF XY: 0.413 AC XY: 13616 AN XY: 32957

African (AFR) AF: 0.509 AC: 15490 AN: 30445

American (AMR) AF: 0.470 AC: 4867 AN: 10364

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1109 AN: 2626

East Asian (EAS) AF: 0.376 AC: 1305 AN: 3472

South Asian (SAS) AF: 0.303 AC: 798 AN: 2634

European-Finnish (FIN) AF: 0.350 AC: 2063 AN: 5894

Middle Eastern (MID) AF: 0.394 AC: 84 AN: 213

European-Non Finnish (NFE) AF: 0.383 AC: 20219 AN: 52845

Other (OTH) AF: 0.451 AC: 681 AN: 1510

Alfa AF: 0.429 Hom.: 7306

Bravo AF: 0.441

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.52
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs5907306; hg19: chrX-141596262;