chrX-43893123-T-C

Variant names:

• chrX-43893123-T-C
• rs1183035

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 0.0803 in 111,847 control chromosomes in the GnomAD database, including 321 homozygotes. There are 2,609 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 0.080 (321 hom., 2609 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 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: 0.0804 AC: 8984 AN: 111795 Hom.: 321 Cov.: 23

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.0587

Gnomad AMR AF: 0.0799

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0252

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.0911

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

GnomAD4 genome AF: 0.0803 AC: 8985 AN: 111847 Hom.: 321 Cov.: 23 AF XY: 0.0767 AC XY: 2609 AN XY: 34011

African (AFR) AF: 0.0159 AC: 491 AN: 30873

American (AMR) AF: 0.0798 AC: 842 AN: 10554

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 359 AN: 2642

East Asian (EAS) AF: 0.00 AC: 0 AN: 3561

South Asian (SAS) AF: 0.0252 AC: 68 AN: 2694

European-Finnish (FIN) AF: 0.124 AC: 742 AN: 6006

Middle Eastern (MID) AF: 0.130 AC: 28 AN: 216

European-Non Finnish (NFE) AF: 0.118 AC: 6278 AN: 53096

Other (OTH) AF: 0.0900 AC: 137 AN: 1523

Alfa AF: 0.0705 Hom.: 1080

Bravo AF: 0.0750

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.80
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs1183035; hg19: chrX-43752369;