X-3224334-T-C

Variant names:

• chrX-3224334-T-C
• rs17051551

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 0.25 in 110,565 control chromosomes in the GnomAD database, including 2,538 homozygotes. There are 8,057 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 0.25 (2538 hom., 8057 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.346 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: 0.250 AC: 27611 AN: 110511 Hom.: 2543 Cov.: 22

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.0403

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.243

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.250 AC: 27617 AN: 110565 Hom.: 2538 Cov.: 22 AF XY: 0.245 AC XY: 8057 AN XY: 32839

African (AFR) AF: 0.251 AC: 7641 AN: 30403

American (AMR) AF: 0.248 AC: 2585 AN: 10420

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 762 AN: 2628

East Asian (EAS) AF: 0.0401 AC: 141 AN: 3513

South Asian (SAS) AF: 0.366 AC: 936 AN: 2559

European-Finnish (FIN) AF: 0.298 AC: 1731 AN: 5818

Middle Eastern (MID) AF: 0.252 AC: 54 AN: 214

European-Non Finnish (NFE) AF: 0.252 AC: 13302 AN: 52809

Other (OTH) AF: 0.245 AC: 373 AN: 1522

Alfa AF: 0.245 Hom.: 26053

Bravo AF: 0.245

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.31
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs17051551; hg19: chrX-3142375;