rs1334995

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.873 AC: 1153 AN: 1320

American (AMR) AF: 0.686 AC: 2464 AN: 3590

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 1687 AN: 1914

East Asian (EAS) AF: 0.635 AC: 1778 AN: 2802

South Asian (SAS) AF: 0.788 AC: 11548 AN: 14660

European-Finnish (FIN) AF: 0.873 AC: 4644 AN: 5320

Middle Eastern (MID) AF: 0.861 AC: 279 AN: 324

European-Non Finnish (NFE) AF: 0.829 AC: 44479 AN: 53684

Other (OTH) AF: 0.826 AC: 3725 AN: 4512

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

African (AFR) AF: 0.858 AC: 35629 AN: 41522

American (AMR) AF: 0.744 AC: 11371 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3060 AN: 3470

East Asian (EAS) AF: 0.666 AC: 3442 AN: 5168

South Asian (SAS) AF: 0.790 AC: 3809 AN: 4820

European-Finnish (FIN) AF: 0.885 AC: 9391 AN: 10610

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56395 AN: 67998

Other (OTH) AF: 0.832 AC: 1758 AN: 2112

Alfa AF: 0.828 Hom.: 26408

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
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs1334995; hg19: chr1-71127061;