chrX-149803773-T-C

Variant names:

• chrX-149803773-T-C
• rs454992

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 0.212 in 111,249 control chromosomes in the GnomAD database, including 1,942 homozygotes. There are 6,761 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 0.21 (1942 hom., 6761 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 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: 0.212 AC: 23579 AN: 111194 Hom.: 1941 Cov.: 23

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.0711

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.214

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.212 AC: 23611 AN: 111249 Hom.: 1942 Cov.: 23 AF XY: 0.202 AC XY: 6761 AN XY: 33513

African (AFR) AF: 0.314 AC: 9536 AN: 30407

American (AMR) AF: 0.133 AC: 1405 AN: 10575

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 556 AN: 2639

East Asian (EAS) AF: 0.0711 AC: 251 AN: 3532

South Asian (SAS) AF: 0.164 AC: 435 AN: 2655

European-Finnish (FIN) AF: 0.191 AC: 1145 AN: 6007

Middle Eastern (MID) AF: 0.216 AC: 47 AN: 218

European-Non Finnish (NFE) AF: 0.187 AC: 9891 AN: 53024

Other (OTH) AF: 0.175 AC: 264 AN: 1511

Alfa AF: 0.193 Hom.: 1313

Bravo AF: 0.210

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.72
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs454992; hg19: chrX-148885435;