rs16894959

chr6-34857885-T-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_017754.4(BLTP3A):c.1735T>C(p.Leu579=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 1,613,712 control chromosomes in the GnomAD database, including 17,853 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 0.17 (2597 hom., cov: 32)
  • Exomes 𝑓: 0.14 (15256 hom.)
• Consequence: BLTP3A NM_017754.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431

Genes affected

BLTP3A (HGNC:21216): (bridge-like lipid transfer protein family member 3A) Enables histone deacetylase binding activity and identical protein binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP7: Synonymous conserved (PhyloP=-0.431 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLTP3A	NM_017754.4	c.1735T>C	p.Leu579=	synonymous_variant	13/21	ENST00000192788.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLTP3A	ENST00000192788.6	c.1735T>C	p.Leu579=	synonymous_variant	13/21	1	NM_017754.4	P1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26422 AN: 151990 Hom.: 2593 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.0809

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.160

GnomAD3 exomes AF: 0.131 AC: 32626 AN: 249234 Hom.: 2642 AF XY: 0.129 AC XY: 17437 AN XY: 135222

Gnomad AFR exome AF: 0.252

Gnomad AMR exome AF: 0.0802

Gnomad ASJ exome AF: 0.155

Gnomad EAS exome AF: 0.0135

Gnomad SAS exome AF: 0.0756

Gnomad FIN exome AF: 0.211

Gnomad NFE exome AF: 0.146

Gnomad OTH exome AF: 0.133

GnomAD4 exome AF: 0.138 AC: 202302 AN: 1461604 Hom.: 15256 Cov.: 33 AF XY: 0.137 AC XY: 99503 AN XY: 727082

Gnomad4 AFR exome AF: 0.260

Gnomad4 AMR exome AF: 0.0860

Gnomad4 ASJ exome AF: 0.156

Gnomad4 EAS exome AF: 0.00658

Gnomad4 SAS exome AF: 0.0772

Gnomad4 FIN exome AF: 0.204

Gnomad4 NFE exome AF: 0.143

Gnomad4 OTH exome AF: 0.138

GnomAD4 genome AF: 0.174 AC: 26440 AN: 152108 Hom.: 2597 Cov.: 32 AF XY: 0.175 AC XY: 12990 AN XY: 74370

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.0110

Gnomad4 SAS AF: 0.0793

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.158

Alfa AF: 0.156 Hom.: 1659

Bravo AF: 0.172

Asia WGS AF: 0.0490 AC: 172 AN: 3478

EpiCase AF: 0.143

EpiControl AF: 0.138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.77
Dann	Benign	0.53

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: rs16894959; hg19: chr6-34825662; COSMIC: COSV51955817;