rs5907306

chrX-142508476-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664519.1(ENSG00000288098):n.443-37905A>G variant causes a intron, non coding transcript 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: ENST00000664519.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.838

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664519.1	n.443-37905A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.424 AC: 46883 AN: 110623 Hom.: 7274 Cov.: 23 AF XY: 0.413 AC XY: 13585 AN XY: 32893

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

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.451

Alfa AF: 0.429 Hom.: 3520

Bravo AF: 0.441

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.5
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5907306; hg19: chrX-141596262;