rs1857030

Variant names:

• chrX-50907893-T-A
• rs1857030

Your query was ambiguous. Multiple possible variants found:

• chrX-50907893-T-A
• chrX-50907893-T-C
• chrX-50907893-T-G

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 0.191 in 103,289 control chromosomes in the GnomAD database, including 2,770 homozygotes. There are 5,152 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 0.19 (2770 hom., 5152 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 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: 0.190 AC: 19660 AN: 103235 Hom.: 2767 Cov.: 22

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.0304

Gnomad AMR AF: 0.0831

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.0521

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0497

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.0681

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.191 AC: 19704 AN: 103289 Hom.: 2770 Cov.: 22 AF XY: 0.181 AC XY: 5152 AN XY: 28477

African (AFR) AF: 0.500 AC: 14222 AN: 28444

American (AMR) AF: 0.0828 AC: 809 AN: 9768

Ashkenazi Jewish (ASJ) AF: 0.0882 AC: 221 AN: 2507

East Asian (EAS) AF: 0.0516 AC: 163 AN: 3157

South Asian (SAS) AF: 0.161 AC: 364 AN: 2257

European-Finnish (FIN) AF: 0.0497 AC: 266 AN: 5349

Middle Eastern (MID) AF: 0.147 AC: 28 AN: 191

European-Non Finnish (NFE) AF: 0.0681 AC: 3379 AN: 49594

Other (OTH) AF: 0.164 AC: 234 AN: 1429

Alfa AF: 0.119 Hom.: 704

Bravo AF: 0.200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.35
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1857030; hg19: chrX-50650893;