rs2190736

Variant names:

• chrX-7878470-G-C
• rs2190736

Your query was ambiguous. Multiple possible variants found:

• chrX-7878470-G-C
• chrX-7878470-G-T

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 0.179 in 110,771 control chromosomes in the GnomAD database, including 1,885 homozygotes. There are 5,863 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 0.18 (1885 hom., 5863 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336
• 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 (EAS) allele frequency at 95% confidence interval = 0.436 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: 0.179 AC: 19858 AN: 110720 Hom.: 1889 Cov.: 22

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.0599

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.0958

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.0882

Gnomad NFE AF: 0.0682

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.179 AC: 19853 AN: 110771 Hom.: 1885 Cov.: 22 AF XY: 0.177 AC XY: 5863 AN XY: 33053

African (AFR) AF: 0.326 AC: 9881 AN: 30348

American (AMR) AF: 0.285 AC: 2974 AN: 10441

Ashkenazi Jewish (ASJ) AF: 0.0958 AC: 253 AN: 2641

East Asian (EAS) AF: 0.455 AC: 1573 AN: 3459

South Asian (SAS) AF: 0.262 AC: 680 AN: 2594

European-Finnish (FIN) AF: 0.0985 AC: 586 AN: 5947

Middle Eastern (MID) AF: 0.0876 AC: 19 AN: 217

European-Non Finnish (NFE) AF: 0.0682 AC: 3610 AN: 52919

Other (OTH) AF: 0.155 AC: 236 AN: 1521

Alfa AF: 0.0207 Hom.: 81

Bravo AF: 0.205

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.80
DANN	Benign	0.28
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2190736; hg19: chrX-7846511;