rs36122347

Variant names:

• chrX-4986142-C-T
• rs36122347

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 0.141 in 110,481 control chromosomes in the GnomAD database, including 905 homozygotes. There are 4,472 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 0.14 (905 hom., 4472 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 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: 0.141 AC: 15548 AN: 110430 Hom.: 902 Cov.: 22

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0772

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.000852

Gnomad SAS AF: 0.0550

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.0909

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.141 AC: 15557 AN: 110481 Hom.: 905 Cov.: 22 AF XY: 0.136 AC XY: 4472 AN XY: 32787

African (AFR) AF: 0.142 AC: 4323 AN: 30438

American (AMR) AF: 0.0771 AC: 801 AN: 10383

Ashkenazi Jewish (ASJ) AF: 0.0919 AC: 242 AN: 2634

East Asian (EAS) AF: 0.000854 AC: 3 AN: 3511

South Asian (SAS) AF: 0.0551 AC: 145 AN: 2630

European-Finnish (FIN) AF: 0.226 AC: 1293 AN: 5727

Middle Eastern (MID) AF: 0.0905 AC: 19 AN: 210

European-Non Finnish (NFE) AF: 0.161 AC: 8487 AN: 52772

Other (OTH) AF: 0.136 AC: 205 AN: 1505

Alfa AF: 0.153 Hom.: 6250

Bravo AF: 0.131

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.34
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs36122347; hg19: chrX-4904183;