rs5977968

Variant names:

• chrX-134189815-T-C
• rs5977968

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 0.189 in 111,301 control chromosomes in the GnomAD database, including 1,900 homozygotes. There are 6,338 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 (1900 hom., 6338 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 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: 0.189 AC: 21037 AN: 111251 Hom.: 1898 Cov.: 23

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0586

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.0675

Gnomad NFE AF: 0.0919

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.189 AC: 21064 AN: 111301 Hom.: 1900 Cov.: 23 AF XY: 0.189 AC XY: 6338 AN XY: 33557

African (AFR) AF: 0.297 AC: 9078 AN: 30561

American (AMR) AF: 0.362 AC: 3773 AN: 10416

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 165 AN: 2641

East Asian (EAS) AF: 0.414 AC: 1452 AN: 3505

South Asian (SAS) AF: 0.300 AC: 796 AN: 2651

European-Finnish (FIN) AF: 0.0985 AC: 596 AN: 6048

Middle Eastern (MID) AF: 0.0553 AC: 12 AN: 217

European-Non Finnish (NFE) AF: 0.0919 AC: 4879 AN: 53070

Other (OTH) AF: 0.181 AC: 273 AN: 1509

Alfa AF: 0.152 Hom.: 4535

Bravo AF: 0.223

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.1
DANN	Benign	0.42
PhyloP100		0.052

Splicing

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

Other links and lift over

dbSNP: rs5977968; hg19: chrX-133323845;