rs16995984

chrX-151489538-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;