rs2271072

Variant names:

• chr1-31367579-C-G
• rs2271072
• NM_004102.5:c.247-85G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004102.5(FABP3):​c.247-85G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 1,123,366 control chromosomes in the GnomAD database, including 188,520 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 0.54 (23383 hom., cov: 32)
  • Exomes 𝑓: 0.57 (165137 hom.)
• Consequence: FABP3 NM_004102.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 11 publications found

Genes affected

FABP3 (HGNC:3557): (fatty acid binding protein 3) The intracellular fatty acid-binding proteins (FABPs) belongs to a multigene family. FABPs are divided into at least three distinct types, namely the hepatic-, intestinal- and cardiac-type. They form 14-15 kDa proteins and are thought to participate in the uptake, intracellular metabolism and/or transport of long-chain fatty acids. They may also be responsible in the modulation of cell growth and proliferation. Fatty acid-binding protein 3 gene contains four exons and its function is to arrest growth of mammary epithelial cells. This gene is a candidate tumor suppressor gene for human breast cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP3	NM_004102.5	c.247-85G>C		intron_variant	Intron 2 of 3	ENST00000373713.7	NP_004093.1
FABP3	NM_001320996.2	c.280-85G>C		intron_variant	Intron 2 of 3		NP_001307925.1
FABP3	XM_011541007.4	c.247-85G>C		intron_variant	Intron 2 of 3		XP_011539309.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP3	ENST00000373713.7	c.247-85G>C		intron_variant	Intron 2 of 3	1	NM_004102.5	ENSP00000362817.2
FABP3	ENST00000482018.1	c.247-85G>C		intron_variant	Intron 4 of 5	5		ENSP00000473982.1
FABP3	ENST00000497275.5	n.207-85G>C		intron_variant	Intron 1 of 2	2
FABP3	ENST00000498148.5	n.*44-85G>C		intron_variant	Intron 3 of 4	2		ENSP00000474078.1

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82650 AN: 151930 Hom.: 23384 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.558

GnomAD4 exome AF: 0.570 AC: 553916 AN: 971318 Hom.: 165137 AF XY: 0.565 AC XY: 284166 AN XY: 503210

African (AFR) AF: 0.461 AC: 11120 AN: 24112

American (AMR) AF: 0.502 AC: 21886 AN: 43638

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 14759 AN: 22732

East Asian (EAS) AF: 0.174 AC: 6534 AN: 37462

South Asian (SAS) AF: 0.370 AC: 28255 AN: 76432

European-Finnish (FIN) AF: 0.582 AC: 29472 AN: 50612

Middle Eastern (MID) AF: 0.588 AC: 2596 AN: 4414

European-Non Finnish (NFE) AF: 0.621 AC: 414341 AN: 667574

Other (OTH) AF: 0.563 AC: 24953 AN: 44342

GnomAD4 genome AF: 0.544 AC: 82656 AN: 152048 Hom.: 23383 Cov.: 32 AF XY: 0.535 AC XY: 39766 AN XY: 74342

African (AFR) AF: 0.462 AC: 19138 AN: 41458

American (AMR) AF: 0.554 AC: 8460 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2223 AN: 3470

East Asian (EAS) AF: 0.190 AC: 983 AN: 5182

South Asian (SAS) AF: 0.351 AC: 1695 AN: 4826

European-Finnish (FIN) AF: 0.571 AC: 6044 AN: 10582

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42309 AN: 67944

Other (OTH) AF: 0.554 AC: 1166 AN: 2106

Alfa AF: 0.593 Hom.: 3386

Bravo AF: 0.540

Asia WGS AF: 0.284 AC: 990 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	1.9
DANN	Benign	0.71
PhyloP100		0.013
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: rs2271072; hg19: chr1-31840426; COSMIC: COSV60001540; COSMIC: COSV60001540;