chr12-100125971-C-T

Variant names:

• chr12-100125971-C-T
• rs7134216
• NM_015054.2:c.44+16621G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BLTP3B	NM_015054.2	c.44+16621G>A		intron_variant	Intron 1 of 20	ENST00000279907.12	NP_055869.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLTP3B	ENST00000279907.12	c.44+16621G>A		intron_variant	Intron 1 of 20	1	NM_015054.2	ENSP00000279907.7
BLTP3B	ENST00000356828.7	c.44+16621G>A		intron_variant	Intron 1 of 12	1		ENSP00000349285.3
BLTP3B	ENST00000547428.1	n.*52+2609G>A		intron_variant	Intron 2 of 3	5		ENSP00000448420.1

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

African (AFR) AF: 0.560 AC: 23195 AN: 41440

American (AMR) AF: 0.171 AC: 2616 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 749 AN: 3472

East Asian (EAS) AF: 0.0598 AC: 309 AN: 5170

South Asian (SAS) AF: 0.186 AC: 895 AN: 4818

European-Finnish (FIN) AF: 0.124 AC: 1311 AN: 10590

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.177 AC: 12005 AN: 67964

Other (OTH) AF: 0.238 AC: 501 AN: 2106

Alfa AF: 0.247 Hom.: 844

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
PhyloP100		-1.0
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: rs7134216; hg19: chr12-100519749;