X-93861388-A-G

Variant names:

• chrX-93861388-A-G
• rs1797020

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 0.159 in 111,050 control chromosomes in the GnomAD database, including 1,164 homozygotes. There are 4,912 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 0.16 (1164 hom., 4912 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.494
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 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: 0.159 AC: 17607 AN: 110998 Hom.: 1162 Cov.: 22

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0991

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.159 AC: 17617 AN: 111050 Hom.: 1164 Cov.: 22 AF XY: 0.148 AC XY: 4912 AN XY: 33284

African (AFR) AF: 0.228 AC: 6959 AN: 30488

American (AMR) AF: 0.111 AC: 1162 AN: 10436

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 502 AN: 2640

East Asian (EAS) AF: 0.206 AC: 717 AN: 3484

South Asian (SAS) AF: 0.107 AC: 282 AN: 2643

European-Finnish (FIN) AF: 0.124 AC: 740 AN: 5970

Middle Eastern (MID) AF: 0.0952 AC: 20 AN: 210

European-Non Finnish (NFE) AF: 0.130 AC: 6881 AN: 52982

Other (OTH) AF: 0.155 AC: 235 AN: 1519

Alfa AF: 0.136 Hom.: 3948

Bravo AF: 0.165

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.89
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs1797020; hg19: chrX-93116387;