ENST00000575148.8:n.404+1333G>T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000575148.8(APOC1P1):​n.404+1333G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00817 in 148,584 control chromosomes in the GnomAD database, including 26 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 0.0082 (26 hom., cov: 30)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00817 (1214/148584) while in subpopulation AFR AF = 0.0287 (1157/40270). AF 95% confidence interval is 0.0274. There are 26 homozygotes in GnomAd4. There are 556 alleles in the male GnomAd4 subpopulation. Median coverage is 30. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 26 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOC1P1	NR_028412.1	n.552+1333G>T		intron_variant	Intron 2 of 2
APOC1P1	NR_028413.1	n.367+1333G>T		intron_variant	Intron 2 of 2
APOC1P1	NR_028414.1	n.244+1333G>T		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>T		intron_variant	Intron 2 of 2	1
APOC1P1	ENST00000507983.7	n.243+1333G>T		intron_variant	Intron 3 of 3	4
APOC1P1	ENST00000571466.3	n.194+1333G>T		intron_variant	Intron 2 of 2	6

Frequencies

GnomAD3 genomes AF: 0.00815 AC: 1210 AN: 148490 Hom.: 26 Cov.: 30

Gnomad AFR AF: 0.0287

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00229

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000216

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.000119

Gnomad OTH AF: 0.00637

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00817 AC: 1214 AN: 148584 Hom.: 26 Cov.: 30 AF XY: 0.00769 AC XY: 556 AN XY: 72332

African (AFR) AF: 0.0287 AC: 1157 AN: 40270

American (AMR) AF: 0.00229 AC: 34 AN: 14856

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 5032

South Asian (SAS) AF: 0.000216 AC: 1 AN: 4626

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

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.000119 AC: 8 AN: 67232

Other (OTH) AF: 0.00632 AC: 13 AN: 2056

Alfa AF: 0.00360 Hom.: 0

Bravo AF: 0.00948

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.61
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;