chrY-13542548-C-G

Variant names:

• chrY-13542548-C-G
• rs11799226

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.096 (0 hom., 3168 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 6 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 (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0961 AC: 3169 AN: 32978 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0645

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0560

Gnomad ASJ AF: 0.00130

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00543

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.0388

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

GnomAD4 genome AF: 0.0959 AC: 3168 AN: 33044 Hom.: 0 Cov.: 0 AF XY: 0.0959 AC XY: 3168 AN XY: 33044

African (AFR) AF: 0.0641 AC: 544 AN: 8482

American (AMR) AF: 0.0559 AC: 198 AN: 3540

Ashkenazi Jewish (ASJ) AF: 0.00130 AC: 1 AN: 771

East Asian (EAS) AF: 0.00 AC: 0 AN: 1283

South Asian (SAS) AF: 0.00 AC: 0 AN: 1503

European-Finnish (FIN) AF: 0.00543 AC: 18 AN: 3314

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 72

European-Non Finnish (NFE) AF: 0.178 AC: 2389 AN: 13396

Other (OTH) AF: 0.0385 AC: 18 AN: 468

Alfa AF: 0.168 Hom.: 2344

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.30
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs11799226; hg19: chrY-15654428;