rs1236440

Variant names:

• chrY-13221267-T-C
• rs1236440

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 0.95 (0 hom., 31091 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.955 AC: 31027 AN: 32495 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.975

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.925

Gnomad OTH AF: 0.943

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: 0.955 AC: 31091 AN: 32559 Hom.: 0 Cov.: 0 AF XY: 0.955 AC XY: 31091 AN XY: 32559

African (AFR) AF: 0.980 AC: 8179 AN: 8345

American (AMR) AF: 0.951 AC: 3357 AN: 3531

Ashkenazi Jewish (ASJ) AF: 0.975 AC: 733 AN: 752

East Asian (EAS) AF: 1.00 AC: 1261 AN: 1261

South Asian (SAS) AF: 1.00 AC: 1412 AN: 1412

European-Finnish (FIN) AF: 0.997 AC: 3190 AN: 3200

Middle Eastern (MID) AF: 0.986 AC: 73 AN: 74

European-Non Finnish (NFE) AF: 0.925 AC: 12311 AN: 13316

Other (OTH) AF: 0.943 AC: 434 AN: 460

Alfa AF: 0.913 Hom.: 44688

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.2
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1236440; hg19: chrY-15333149;