rs5920067

Variant names:

• chrX-146301644-T-C
• rs5920067

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 0.402 in 110,358 control chromosomes in the GnomAD database, including 6,618 homozygotes. There are 13,237 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 0.40 (6618 hom., 13237 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.524 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: 0.402 AC: 44290 AN: 110309 Hom.: 6612 Cov.: 22

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.402 AC: 44319 AN: 110358 Hom.: 6618 Cov.: 22 AF XY: 0.405 AC XY: 13237 AN XY: 32648

African (AFR) AF: 0.289 AC: 8779 AN: 30423

American (AMR) AF: 0.536 AC: 5512 AN: 10292

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1118 AN: 2634

East Asian (EAS) AF: 0.467 AC: 1606 AN: 3439

South Asian (SAS) AF: 0.354 AC: 925 AN: 2612

European-Finnish (FIN) AF: 0.549 AC: 3175 AN: 5780

Middle Eastern (MID) AF: 0.340 AC: 73 AN: 215

European-Non Finnish (NFE) AF: 0.423 AC: 22344 AN: 52777

Other (OTH) AF: 0.412 AC: 621 AN: 1506

Alfa AF: 0.417 Hom.: 13748

Bravo AF: 0.407

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.3
DANN	Benign	0.71
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs5920067; hg19: chrX-145383162;