rs16995984

Variant names:

• chrX-151489538-C-T
• rs16995984
• ENST00000811741.1:n.224-10753G>A

Variant summary

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

The ENST00000811741.1(ENSG00000305574):​n.224-10753G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.065 in 112,058 control chromosomes in the GnomAD database, including 268 homozygotes. There are 1,967 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 0.065 (268 hom., 1967 hem., cov: 23)
• Consequence: ENSG00000305574 ENST00000811741.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498
• Publications: 1 publications found

Genes affected

ENSG00000305574 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 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
ENSG00000305574	ENST00000811741.1	n.224-10753G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0650 AC: 7280 AN: 112002 Hom.: 267 Cov.: 23

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0367

Gnomad AMR AF: 0.0478

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.0471

Gnomad FIN AF: 0.0156

Gnomad MID AF: 0.0508

Gnomad NFE AF: 0.0442

Gnomad OTH AF: 0.0809

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

GnomAD4 genome AF: 0.0650 AC: 7287 AN: 112058 Hom.: 268 Cov.: 23 AF XY: 0.0574 AC XY: 1967 AN XY: 34252

African (AFR) AF: 0.121 AC: 3727 AN: 30796

American (AMR) AF: 0.0478 AC: 507 AN: 10609

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 282 AN: 2644

East Asian (EAS) AF: 0.0112 AC: 40 AN: 3560

South Asian (SAS) AF: 0.0484 AC: 129 AN: 2666

European-Finnish (FIN) AF: 0.0156 AC: 96 AN: 6147

Middle Eastern (MID) AF: 0.0463 AC: 10 AN: 216

European-Non Finnish (NFE) AF: 0.0441 AC: 2349 AN: 53211

Other (OTH) AF: 0.0799 AC: 122 AN: 1527

Alfa AF: 0.0547 Hom.: 2916

Bravo AF: 0.0708

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.44
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs16995984; hg19: chrX-150658010;