19-44926451-G-C

Variant names:

• chr19-44926451-G-C
• rs60049679
• ENST00000795568.1:n.236+275G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000795568.1(APOC1P1):​n.236+275G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 151,952 control chromosomes in the GnomAD database, including 991 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 0.11 (991 hom., cov: 30)
• Consequence: APOC1P1 ENST00000795568.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188
• Publications: 17 publications found

Genes affected

APOC1P1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 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
APOC1P1	ENST00000795568.1	n.236+275G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16156 AN: 151832 Hom.: 987 Cov.: 30

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0673

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0785

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.107 AC: 16190 AN: 151952 Hom.: 991 Cov.: 30 AF XY: 0.113 AC XY: 8393 AN XY: 74262

African (AFR) AF: 0.110 AC: 4579 AN: 41464

American (AMR) AF: 0.140 AC: 2134 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0673 AC: 233 AN: 3464

East Asian (EAS) AF: 0.150 AC: 774 AN: 5156

South Asian (SAS) AF: 0.183 AC: 882 AN: 4810

European-Finnish (FIN) AF: 0.179 AC: 1888 AN: 10550

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0785 AC: 5336 AN: 67950

Other (OTH) AF: 0.0952 AC: 201 AN: 2112

Alfa AF: 0.0267 Hom.: 26

Bravo AF: 0.105

Asia WGS AF: 0.184 AC: 643 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.18
DANN	Benign	0.43
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs60049679; hg19: chr19-45429708;