Y-13221267-T-C

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).

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: 0.955 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 v4.3

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;