rs428295

Variant names:

• chr22-21358280-T-A
• rs428295

Your query was ambiguous. Multiple possible variants found:

• chr22-21358280-T-A
• chr22-21358280-T-C

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 0.0 (0 hom., cov: 8)
  • Failed GnomAD Quality Control
• Consequence: CA15P3 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.933
• Publications: 1 publications found

Genes affected

CA15P3 (HGNC:44363): (CA15 pseudogene 3)

LINC01651 (HGNC:52439): (long intergenic non-protein coding RNA 1651)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CA15P3		n.21358280T>A		intragenic_variant
LINC01651	NR_170329.1	n.*213T>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01651	ENST00000666255.1	n.*213T>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 51334 Hom.: 0 Cov.: 8

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 51334 Hom.: 0 Cov.: 8 AF XY: 0.00 AC XY: 0 AN XY: 22968

African (AFR) AF: 0.00 AC: 0 AN: 11012

American (AMR) AF: 0.00 AC: 0 AN: 4750

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1458

East Asian (EAS) AF: 0.00 AC: 0 AN: 1900

South Asian (SAS) AF: 0.00 AC: 0 AN: 1688

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2866

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 148

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 26566

Other (OTH) AF: 0.00 AC: 0 AN: 578

Alfa AF: 0.00 Hom.: 2606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.8
DANN	Benign	0.39
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs428295; hg19: chr22-21712569;