rs16909318

Positions:

• chr8-81532989-C-A

Variant summary

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

The NM_001105281.6(FABP12):​c.-76+813G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0945 in 152,212 control chromosomes in the GnomAD database, including 716 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 0.094 (716 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FABP12 NM_001105281.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

Genes affected

FABP12 (HGNC:34524): (fatty acid binding protein 12) Predicted to enable lipid binding activity. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000253374 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FABP12	NM_001105281.6	c.-76+813G>T		intron_variant			NP_001098751.1
FABP12	XM_006716465.4	c.-59+813G>T		intron_variant			XP_006716528.1
FABP12	XM_011517577.3	c.-58-1616G>T		intron_variant			XP_011515879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FABP12	ENST00000360464.6	c.-76+813G>T		intron_variant		1		ENSP00000353650.4
FABP12	ENST00000692030.1	c.-58-1616G>T		intron_variant				ENSP00000510293.1
ENSG00000253374	ENST00000523380.5	n.573C>A		non_coding_transcript_exon_variant	4/4	5

Frequencies

GnomAD3 genomes AF: 0.0944 AC: 14361 AN: 152094 Hom.: 712 Cov.: 33

Gnomad AFR AF: 0.0552

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.0794

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0846

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0817

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0945 AC: 14383 AN: 152212 Hom.: 716 Cov.: 33 AF XY: 0.0956 AC XY: 7117 AN XY: 74410

Gnomad4 AFR AF: 0.0551

Gnomad4 AMR AF: 0.0797

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.0849

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0837

Alfa AF: 0.107 Hom.: 1459

Bravo AF: 0.0875

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16909318; hg19: chr8-82445224;