X-877981-T-G

Variant names:

• chrX-877981-T-G
• rs7053485

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 0.104 in 152,096 control chromosomes in the GnomAD database, including 870 homozygotes. There are 7,894 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 0.10 (870 hom., 7894 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 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: 0.104 AC: 15848 AN: 151980 Hom.: 873 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0989

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.0798

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0993

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.104 AC: 15842 AN: 152096 Hom.: 870 Cov.: 32 AF XY: 0.106 AC XY: 7894 AN XY: 74338

African (AFR) AF: 0.114 AC: 4743 AN: 41468

American (AMR) AF: 0.0989 AC: 1511 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0611 AC: 212 AN: 3472

East Asian (EAS) AF: 0.0794 AC: 411 AN: 5176

South Asian (SAS) AF: 0.108 AC: 520 AN: 4826

European-Finnish (FIN) AF: 0.130 AC: 1379 AN: 10570

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0993 AC: 6749 AN: 67984

Other (OTH) AF: 0.109 AC: 231 AN: 2110

Bravo AF: 0.101

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.88
DANN	Benign	0.44
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7053485; hg19: chrX-838716;