rs891407

Variant names:

• chrY-19681204-G-C
• rs891407

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.59 (0 hom., 19485 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 5 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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: 0.590 AC: 19412 AN: 32911 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.566

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.591 AC: 19485 AN: 32977 Hom.: 0 Cov.: 0 AF XY: 0.591 AC XY: 19485 AN XY: 32977

African (AFR) AF: 0.794 AC: 6672 AN: 8399

American (AMR) AF: 0.503 AC: 1859 AN: 3694

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 602 AN: 752

East Asian (EAS) AF: 0.996 AC: 1190 AN: 1195

South Asian (SAS) AF: 0.535 AC: 774 AN: 1448

European-Finnish (FIN) AF: 0.935 AC: 3123 AN: 3340

Middle Eastern (MID) AF: 0.958 AC: 69 AN: 72

European-Non Finnish (NFE) AF: 0.364 AC: 4878 AN: 13406

Other (OTH) AF: 0.574 AC: 265 AN: 462

Alfa AF: 0.394 Hom.: 5153

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.29
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs891407; hg19: chrY-21843090;