chrX-146274030-T-C

Variant names:

• chrX-146274030-T-C
• rs12014291

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 0.485 in 109,631 control chromosomes in the GnomAD database, including 9,520 homozygotes. There are 15,223 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 0.48 (9520 hom., 15223 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.56 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: 0.484 AC: 53094 AN: 109587 Hom.: 9515 Cov.: 22

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.466

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.485 AC: 53150 AN: 109631 Hom.: 9520 Cov.: 22 AF XY: 0.476 AC XY: 15223 AN XY: 31961

African (AFR) AF: 0.552 AC: 16650 AN: 30155

American (AMR) AF: 0.573 AC: 5877 AN: 10262

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1164 AN: 2613

East Asian (EAS) AF: 0.336 AC: 1164 AN: 3461

South Asian (SAS) AF: 0.428 AC: 1095 AN: 2560

European-Finnish (FIN) AF: 0.461 AC: 2613 AN: 5667

Middle Eastern (MID) AF: 0.481 AC: 102 AN: 212

European-Non Finnish (NFE) AF: 0.445 AC: 23382 AN: 52542

Other (OTH) AF: 0.487 AC: 727 AN: 1492

Alfa AF: 0.467 Hom.: 42990

Bravo AF: 0.506

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.34
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs12014291; hg19: chrX-145355548;