chr12-109864465-C-T

Variant names:

• chr12-109864465-C-T
• rs7966820
• NM_016433.4:c.104-5724G>A

Variant summary

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

The NM_016433.4(GLTP):​c.104-5724G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,992 control chromosomes in the GnomAD database, including 23,294 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 0.55 (23294 hom., cov: 32)
• Consequence: GLTP NM_016433.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 16 publications found

Genes affected

GLTP (HGNC:24867): (glycolipid transfer protein) The protein encoded by this gene is similar to bovine and porcine proteins which accelerate transfer of certain glycosphingolipids and glyceroglycolipids between membranes. It is thought to be a cytoplasmic protein. [provided by RefSeq, Jul 2008]

ENSG00000302242 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLTP	NM_016433.4	c.104-5724G>A		intron_variant	Intron 1 of 4	ENST00000318348.9	NP_057517.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLTP	ENST00000318348.9	c.104-5724G>A		intron_variant	Intron 1 of 4	1	NM_016433.4	ENSP00000315263.3

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82970 AN: 151872 Hom.: 23267 Cov.: 32

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.546 AC: 83056 AN: 151992 Hom.: 23294 Cov.: 32 AF XY: 0.548 AC XY: 40742 AN XY: 74284

African (AFR) AF: 0.550 AC: 22785 AN: 41422

American (AMR) AF: 0.641 AC: 9780 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1729 AN: 3468

East Asian (EAS) AF: 0.161 AC: 836 AN: 5184

South Asian (SAS) AF: 0.657 AC: 3165 AN: 4820

European-Finnish (FIN) AF: 0.586 AC: 6191 AN: 10558

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36861 AN: 67964

Other (OTH) AF: 0.541 AC: 1144 AN: 2116

Alfa AF: 0.551 Hom.: 13424

Bravo AF: 0.541

Asia WGS AF: 0.470 AC: 1636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.77
DANN	Benign	0.49
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7966820; hg19: chr12-110302270;