rs16983007

Variant names:

• chrX-24351161-C-T
• rs16983007

Variant summary

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

The variant allele was found at a frequency of 0.138 in 111,270 control chromosomes in the GnomAD database, including 1,272 homozygotes. There are 4,368 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 0.14 (1272 hom., 4368 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 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: 0.138 AC: 15339 AN: 111219 Hom.: 1270 Cov.: 23

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.0438

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.0729

Gnomad SAS AF: 0.0477

Gnomad FIN AF: 0.0728

Gnomad MID AF: 0.0546

Gnomad NFE AF: 0.0563

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.138 AC: 15365 AN: 111270 Hom.: 1272 Cov.: 23 AF XY: 0.130 AC XY: 4368 AN XY: 33500

African (AFR) AF: 0.309 AC: 9388 AN: 30399

American (AMR) AF: 0.160 AC: 1670 AN: 10468

Ashkenazi Jewish (ASJ) AF: 0.0885 AC: 234 AN: 2645

East Asian (EAS) AF: 0.0728 AC: 260 AN: 3570

South Asian (SAS) AF: 0.0478 AC: 129 AN: 2698

European-Finnish (FIN) AF: 0.0728 AC: 435 AN: 5974

Middle Eastern (MID) AF: 0.0599 AC: 13 AN: 217

European-Non Finnish (NFE) AF: 0.0564 AC: 2994 AN: 53093

Other (OTH) AF: 0.139 AC: 212 AN: 1521

Alfa AF: 0.114 Hom.: 831

Bravo AF: 0.153

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	5.1
DANN	Benign	0.87
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs16983007; hg19: chrX-24369278;