chrX-70054810-G-T

Variant names:

• chrX-70054810-G-T
• rs1327476

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 0.373 in 109,999 control chromosomes in the GnomAD database, including 5,617 homozygotes. There are 11,989 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 0.37 (5617 hom., 11989 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97
• Publications: 2 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 = 0.492 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: 0.372 AC: 40951 AN: 109942 Hom.: 5603 Cov.: 22

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.373 AC: 40979 AN: 109999 Hom.: 5617 Cov.: 22 AF XY: 0.371 AC XY: 11989 AN XY: 32315

African (AFR) AF: 0.285 AC: 8603 AN: 30227

American (AMR) AF: 0.504 AC: 5182 AN: 10288

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1007 AN: 2625

East Asian (EAS) AF: 0.504 AC: 1754 AN: 3482

South Asian (SAS) AF: 0.495 AC: 1254 AN: 2532

European-Finnish (FIN) AF: 0.389 AC: 2236 AN: 5747

Middle Eastern (MID) AF: 0.363 AC: 77 AN: 212

European-Non Finnish (NFE) AF: 0.378 AC: 19923 AN: 52718

Other (OTH) AF: 0.396 AC: 593 AN: 1497

Alfa AF: 0.391 Hom.: 23460

Bravo AF: 0.386

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	12
DANN	Benign	0.63
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs1327476; hg19: chrX-69274660;