Y-12881443-A-G

Variant names:

• chrY-12881443-A-G
• rs11799152

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

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 0.025 (0 hom., 765 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.025 (765/30617) while in subpopulation AMR AF = 0.0521 (168/3225). AF 95% confidence interval is 0.0457. There are 0 homozygotes in GnomAd4. There are 765 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Hemizygotes in GnomAd4 at 765 gene

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: 0.0250 AC: 763 AN: 30554 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00483

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.0522

Gnomad ASJ AF: 0.0774

Gnomad EAS AF: 0.000842

Gnomad SAS AF: 0.0275

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.200

Gnomad NFE AF: 0.0323

Gnomad OTH AF: 0.0242

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

GnomAD4 genome AF: 0.0250 AC: 765 AN: 30617 Hom.: 0 Cov.: 0 AF XY: 0.0250 AC XY: 765 AN XY: 30617

African (AFR) AF: 0.00479 AC: 37 AN: 7718

American (AMR) AF: 0.0521 AC: 168 AN: 3225

Ashkenazi Jewish (ASJ) AF: 0.0774 AC: 57 AN: 736

East Asian (EAS) AF: 0.000842 AC: 1 AN: 1187

South Asian (SAS) AF: 0.0282 AC: 36 AN: 1277

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3050

Middle Eastern (MID) AF: 0.191 AC: 13 AN: 68

European-Non Finnish (NFE) AF: 0.0325 AC: 414 AN: 12737

Other (OTH) AF: 0.0241 AC: 10 AN: 415

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.8
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs11799152; hg19: chrY-14993358;