X-123182584-T-C

Variant names:

• chrX-123182584-T-C
• rs3761555

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 0.382 in 110,353 control chromosomes in the GnomAD database, including 6,552 homozygotes. There are 12,451 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 0.38 (6552 hom., 12451 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 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: 0.381 AC: 42065 AN: 110299 Hom.: 6543 Cov.: 22

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.382 AC: 42115 AN: 110353 Hom.: 6552 Cov.: 22 AF XY: 0.380 AC XY: 12451 AN XY: 32737

African (AFR) AF: 0.519 AC: 15731 AN: 30321

American (AMR) AF: 0.558 AC: 5829 AN: 10453

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 880 AN: 2619

East Asian (EAS) AF: 0.640 AC: 2211 AN: 3454

South Asian (SAS) AF: 0.400 AC: 1040 AN: 2599

European-Finnish (FIN) AF: 0.269 AC: 1580 AN: 5864

Middle Eastern (MID) AF: 0.456 AC: 98 AN: 215

European-Non Finnish (NFE) AF: 0.266 AC: 13996 AN: 52653

Other (OTH) AF: 0.409 AC: 611 AN: 1495

Alfa AF: 0.329 Hom.: 26619

Bravo AF: 0.415

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	8.1
DANN	Benign	0.81
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs3761555; hg19: chrX-122316437;