rs7259004

Positions:

• chr19-44929300-G-C
• chr19-44929300-G-T

Variant summary

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

The NR_028412.1(APOC1P1):​n.552+1370G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 151,480 control chromosomes in the GnomAD database, including 2,665 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 0.16 (2665 hom., cov: 30)
• Consequence: APOC1P1 NR_028412.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOC1P1	NR_028412.1	n.552+1370G>C		intron_variant, non_coding_transcript_variant
APOC1P1	NR_028413.1	n.367+1370G>C		intron_variant, non_coding_transcript_variant
APOC1P1	NR_028414.1	n.244+1370G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOC1P1	ENST00000571466.3	n.194+1370G>C		intron_variant, non_coding_transcript_variant
APOC1P1	ENST00000701959.1	n.245+1370G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24773 AN: 151364 Hom.: 2656 Cov.: 30

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0394

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.164 AC: 24806 AN: 151480 Hom.: 2665 Cov.: 30 AF XY: 0.163 AC XY: 12086 AN XY: 74016

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.0394

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.158

Alfa AF: 0.0428 Hom.: 40

Bravo AF: 0.178

Asia WGS AF: 0.264 AC: 918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7259004; hg19: chr19-45432557;