rs4766642

Positions:

• chr12-109875949-T-C

Variant summary

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

The NM_016433.4(GLTP):​c.103+4323A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 152,138 control chromosomes in the GnomAD database, including 32,366 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 0.64 (32366 hom., cov: 33)
• Consequence: GLTP NM_016433.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLTP	NM_016433.4	c.103+4323A>G		intron_variant		ENST00000318348.9	NP_057517.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLTP	ENST00000318348.9	c.103+4323A>G		intron_variant		1	NM_016433.4	ENSP00000315263.3

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97824 AN: 152020 Hom.: 32318 Cov.: 33

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.644 AC: 97932 AN: 152138 Hom.: 32366 Cov.: 33 AF XY: 0.646 AC XY: 48032 AN XY: 74360

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.622

Alfa AF: 0.614 Hom.: 6510

Bravo AF: 0.644

Asia WGS AF: 0.605 AC: 2103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.53
DANN	Benign	0.71

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

Publications

LitVar

Other links and lift over

dbSNP: rs4766642; hg19: chr12-110313754;