rs1334995

Variant names:

• chr1-70661378-A-G
• rs1334995
• ENST00000446037.2:n.-113T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000446037.2(CASP3P1):​n.-113T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 240,310 control chromosomes in the GnomAD database, including 81,760 homozygotes. 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 0.83 (52263 hom., cov: 32)
  • Exomes 𝑓: 0.81 (29497 hom.)
• Consequence: CASP3P1 ENST00000446037.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

Genes affected

CASP3P1 (HGNC:43596): (caspase 3 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

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
CASP3P1	ENST00000446037.2	n.-113T>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125780 AN: 152066 Hom.: 52216 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.836

GnomAD4 exome AF: 0.814 AC: 71757 AN: 88126 Hom.: 29497 AF XY: 0.813 AC XY: 39399 AN XY: 48464

Gnomad4 AFR exome AF: 0.873

Gnomad4 AMR exome AF: 0.686

Gnomad4 ASJ exome AF: 0.881

Gnomad4 EAS exome AF: 0.635

Gnomad4 SAS exome AF: 0.788

Gnomad4 FIN exome AF: 0.873

Gnomad4 NFE exome AF: 0.829

Gnomad4 OTH exome AF: 0.826

GnomAD4 genome AF: 0.827 AC: 125885 AN: 152184 Hom.: 52263 Cov.: 32 AF XY: 0.828 AC XY: 61610 AN XY: 74412

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.829

Gnomad4 OTH AF: 0.832

Alfa AF: 0.828 Hom.: 23756

Bravo AF: 0.813

Asia WGS AF: 0.744 AC: 2587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.5
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1334995; hg19: chr1-71127061;