rs7258987

Variant names:

• chr19-44929263-G-A
• rs7258987
• ENST00000575148.8:n.404+1333G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-44929263-G-A
• chr19-44929263-G-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000575148.8(APOC1P1):​n.404+1333G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: 30)
  • Failed GnomAD Quality Control
• Consequence: APOC1P1 ENST00000575148.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 2 publications found

Genes affected

APOC1P1 (HGNC:):

APOC1P1 (HGNC:608): (apolipoprotein C1 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOC1P1	NR_028412.1	n.552+1333G>A		intron_variant	Intron 2 of 2
APOC1P1	NR_028413.1	n.367+1333G>A		intron_variant	Intron 2 of 2
APOC1P1	NR_028414.1	n.244+1333G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOC1P1	ENST00000575148.8	n.404+1333G>A		intron_variant	Intron 2 of 2	1
APOC1P1	ENST00000507983.7	n.243+1333G>A		intron_variant	Intron 3 of 3	4
APOC1P1	ENST00000571466.3	n.194+1333G>A		intron_variant	Intron 2 of 2	6

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 148492 Hom.: 0 Cov.: 30

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: 148492 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 72220

African (AFR) AF: 0.00 AC: 0 AN: 40166

American (AMR) AF: 0.00 AC: 0 AN: 14840

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3438

East Asian (EAS) AF: 0.00 AC: 0 AN: 5042

South Asian (SAS) AF: 0.00 AC: 0 AN: 4632

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9882

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67238

Other (OTH) AF: 0.00 AC: 0 AN: 2040

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.71
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs7258987; hg19: chr19-45432520;