rs4825066

Variant names:

• chrX-142065546-G-A
• rs4825066
• ENST00000664519.1:n.223-130161G>A

Variant summary

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

The ENST00000664519.1(ENSG00000288098):​n.223-130161G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 110,343 control chromosomes in the GnomAD database, including 6,361 homozygotes. There are 12,727 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 0.40 (6361 hom., 12727 hem., cov: 23)
• Consequence: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.693

Genes affected

ENSG00000288098 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.469 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
ENSG00000288098	ENST00000664519.1	n.223-130161G>A		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.397 AC: 43763 AN: 110295 Hom.: 6369 Cov.: 23 AF XY: 0.389 AC XY: 12696 AN XY: 32651

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.397 AC: 43781 AN: 110343 Hom.: 6361 Cov.: 23 AF XY: 0.389 AC XY: 12727 AN XY: 32709

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.437

Alfa AF: 0.387 Hom.: 2566

Bravo AF: 0.416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.080
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4825066; hg19: chrX-141153332;