rs16995984

Variant names:

• chrX-151489538-C-T
• rs16995984

Variant summary

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

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498

ACMG classification

Verdict is Benign. Variant got -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

Frequencies

GnomAD3 genomes AF: 0.0650 AC: 7280 AN: 112002 Hom.: 267 Cov.: 23 AF XY: 0.0574 AC XY: 1962 AN XY: 34186

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

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.0478

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.0112

Gnomad4 SAS AF: 0.0484

Gnomad4 FIN AF: 0.0156

Gnomad4 NFE AF: 0.0441

Gnomad4 OTH AF: 0.0799

Alfa AF: 0.0505 Hom.: 1807

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16995984; hg19: chrX-150658010;