X-151677903-T-G

Variant names:

• chrX-151677903-T-G
• rs7878232

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 0.209 in 111,913 control chromosomes in the GnomAD database, including 1,918 homozygotes. There are 6,914 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 0.21 (1918 hom., 6914 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.683
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.294 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: 0.209 AC: 23356 AN: 111861 Hom.: 1916 Cov.: 24

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.0843

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.209 AC: 23364 AN: 111913 Hom.: 1918 Cov.: 24 AF XY: 0.203 AC XY: 6914 AN XY: 34129

African (AFR) AF: 0.132 AC: 4082 AN: 30837

American (AMR) AF: 0.303 AC: 3223 AN: 10651

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 867 AN: 2640

East Asian (EAS) AF: 0.0843 AC: 298 AN: 3535

South Asian (SAS) AF: 0.234 AC: 625 AN: 2668

European-Finnish (FIN) AF: 0.201 AC: 1228 AN: 6111

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

European-Non Finnish (NFE) AF: 0.235 AC: 12483 AN: 53062

Other (OTH) AF: 0.247 AC: 374 AN: 1517

Alfa AF: 0.197 Hom.: 3222

Bravo AF: 0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.47
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs7878232; hg19: chrX-150846375;