chrX-141994899-A-G

Variant names:

• chrX-141994899-A-G
• rs17407
• ENST00000664519.1:n.222+60182A>G

Variant summary

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

The ENST00000664519.1(ENSG00000288098):​n.222+60182A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 111,425 control chromosomes in the GnomAD database, including 4,702 homozygotes. There are 9,933 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 0.32 (4702 hom., 9933 hem., cov: 23)
• Consequence: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 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.222+60182A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 35628 AN: 111370 Hom.: 4699 Cov.: 23

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.00167

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.432

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.320 AC: 35643 AN: 111425 Hom.: 4702 Cov.: 23 AF XY: 0.295 AC XY: 9933 AN XY: 33667

African (AFR) AF: 0.270 AC: 8289 AN: 30653

American (AMR) AF: 0.250 AC: 2635 AN: 10526

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1407 AN: 2640

East Asian (EAS) AF: 0.00168 AC: 6 AN: 3576

South Asian (SAS) AF: 0.117 AC: 315 AN: 2699

European-Finnish (FIN) AF: 0.233 AC: 1399 AN: 5997

Middle Eastern (MID) AF: 0.441 AC: 94 AN: 213

European-Non Finnish (NFE) AF: 0.392 AC: 20761 AN: 52940

Other (OTH) AF: 0.330 AC: 497 AN: 1506

Alfa AF: 0.364 Hom.: 30338

Bravo AF: 0.319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.089
DANN	Benign	0.72
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs17407; hg19: chrX-141082685;