X-146281805-G-C

Variant names:

• chrX-146281805-G-C
• rs1339485

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 0.422 in 110,353 control chromosomes in the GnomAD database, including 7,544 homozygotes. There are 13,369 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 0.42 (7544 hom., 13369 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 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: 0.422 AC: 46496 AN: 110306 Hom.: 7538 Cov.: 23

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.353

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.422 AC: 46558 AN: 110353 Hom.: 7544 Cov.: 23 AF XY: 0.409 AC XY: 13369 AN XY: 32675

African (AFR) AF: 0.542 AC: 16494 AN: 30408

American (AMR) AF: 0.528 AC: 5456 AN: 10334

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 883 AN: 2638

East Asian (EAS) AF: 0.338 AC: 1171 AN: 3464

South Asian (SAS) AF: 0.325 AC: 860 AN: 2648

European-Finnish (FIN) AF: 0.341 AC: 1952 AN: 5718

Middle Eastern (MID) AF: 0.374 AC: 80 AN: 214

European-Non Finnish (NFE) AF: 0.355 AC: 18723 AN: 52753

Other (OTH) AF: 0.423 AC: 639 AN: 1509

Alfa AF: 0.400 Hom.: 2614

Bravo AF: 0.451

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.44
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1339485; hg19: chrX-145363323;