rs7134216

Positions:

• chr12-100125971-C-T

Variant summary

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

The NM_015054.2(BLTP3B):​c.44+16621G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,020 control chromosomes in the GnomAD database, including 8,241 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 0.28 (8241 hom., cov: 32)
• Consequence: BLTP3B NM_015054.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

BLTP3B (HGNC:29102): (bridge-like lipid transfer protein family member 3B) Enables GARP complex binding activity and protein homodimerization activity. Located in cytosol and early endosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLTP3B	NM_015054.2	c.44+16621G>A		intron_variant		ENST00000279907.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLTP3B	ENST00000279907.12	c.44+16621G>A		intron_variant		1	NM_015054.2	P1
BLTP3B	ENST00000356828.7	c.44+16621G>A		intron_variant		1
BLTP3B	ENST00000547428.1	c.*52+2609G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41765 AN: 151902 Hom.: 8208 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0600

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.275 AC: 41854 AN: 152020 Hom.: 8241 Cov.: 32 AF XY: 0.267 AC XY: 19863 AN XY: 74320

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.0598

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.238

Alfa AF: 0.234 Hom.: 730

Bravo AF: 0.291

Asia WGS AF: 0.180 AC: 625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.091
DANN	Benign	0.52

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: rs7134216; hg19: chr12-100519749;