chrX-891996-G-T

Variant names:

• chrX-891996-G-T
• rs4497142

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 0.122 in 152,032 control chromosomes in the GnomAD database, including 2,997 homozygotes. There are 8,960 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 0.12 (2997 hom., 8960 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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: 0.122 AC: 18523 AN: 151914 Hom.: 2978 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.00331

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.0325

Gnomad SAS AF: 0.0392

Gnomad FIN AF: 0.0269

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0105

Gnomad OTH AF: 0.0957

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

GnomAD4 genome AF: 0.122 AC: 18584 AN: 152032 Hom.: 2997 Cov.: 32 AF XY: 0.121 AC XY: 8960 AN XY: 74324

African (AFR) AF: 0.365 AC: 15105 AN: 41416

American (AMR) AF: 0.118 AC: 1802 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0280 AC: 97 AN: 3470

East Asian (EAS) AF: 0.0325 AC: 168 AN: 5162

South Asian (SAS) AF: 0.0392 AC: 189 AN: 4818

European-Finnish (FIN) AF: 0.0269 AC: 285 AN: 10586

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0105 AC: 711 AN: 68014

Other (OTH) AF: 0.0971 AC: 205 AN: 2112

Bravo AF: 0.143

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.27
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4497142; hg19: chrX-852731;