chr4-119319647-C-CATAATAATAATA

Variant names:

• chr4-119319647-C-CATAATAATAATA
• rs71595363
• NM_000134.4:c.241-16_241-5dupTATTATTATTAT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP6_Very_Strong

The NM_000134.4(FABP2):​c.241-16_241-5dupTATTATTATTAT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.070 (491 hom., cov: 0)
  • Exomes 𝑓: 0.021 (228 hom.)
  • Failed GnomAD Quality Control
• Consequence: FABP2 NM_000134.4 splice_region, intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.118
• Publications: 3 publications found

Genes affected

FABP2 (HGNC:3556): (fatty acid binding protein 2) The protein encoded by this gene is an intracellular fatty acid-binding protein that participates in the uptake, intracellular metabolism, and transport of long-chain fatty acids. The encoded protein is also involved in the modulation of cell growth and proliferation. This protein binds saturated long-chain fatty acids with high affinity, and may act as a lipid sensor to maintain energy homeostasis. [provided by RefSeq, Aug 2017]

ENSG00000294020 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP6: Variant 4-119319647-C-CATAATAATAATA is Benign according to our data. Variant chr4-119319647-C-CATAATAATAATA is described in ClinVar as Benign. ClinVar VariationId is 767974.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000134.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP2	NM_000134.4	MANE Select	c.241-16_241-5dupTATTATTATTAT		splice_region intron	N/A	NP_000125.2	P12104

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP2	ENST00000274024.4	TSL:1 MANE Select	c.241-5_241-4insTATTATTATTAT		splice_region intron	N/A	ENSP00000274024.3	P12104
	ENSG00000294020	ENST00000720595.1		n.176-14681_176-14680insATAATAATAATA		intron	N/A
	ENSG00000294020	ENST00000720596.1		n.224-14681_224-14680insATAATAATAATA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0700 AC: 10128 AN: 144760 Hom.: 488 Cov.: 0

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0580

Gnomad ASJ AF: 0.0284

Gnomad EAS AF: 0.0376

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0467

Gnomad MID AF: 0.0296

Gnomad NFE AF: 0.0430

Gnomad OTH AF: 0.0705

GnomAD2 exomes AF: 0.0204 AC: 1530 AN: 75038 AF XY: 0.0200

Gnomad AFR exome AF: 0.0212

Gnomad AMR exome AF: 0.0119

Gnomad ASJ exome AF: 0.0237

Gnomad EAS exome AF: 0.0125

Gnomad FIN exome AF: 0.0251

Gnomad NFE exome AF: 0.0227

Gnomad OTH exome AF: 0.0248

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0211 AC: 13722 AN: 650314 Hom.: 228 Cov.: 12 AF XY: 0.0216 AC XY: 7285 AN XY: 336682

African (AFR) AF: 0.0741 AC: 936 AN: 12638

American (AMR) AF: 0.0217 AC: 315 AN: 14516

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 281 AN: 15944

East Asian (EAS) AF: 0.0173 AC: 383 AN: 22186

South Asian (SAS) AF: 0.00735 AC: 269 AN: 36592

European-Finnish (FIN) AF: 0.0217 AC: 612 AN: 28240

Middle Eastern (MID) AF: 0.00919 AC: 20 AN: 2176

European-Non Finnish (NFE) AF: 0.0208 AC: 10152 AN: 488904

Other (OTH) AF: 0.0259 AC: 754 AN: 29118

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0701 AC: 10149 AN: 144772 Hom.: 491 Cov.: 0 AF XY: 0.0711 AC XY: 4994 AN XY: 70214

African (AFR) AF: 0.138 AC: 5463 AN: 39622

American (AMR) AF: 0.0581 AC: 831 AN: 14298

Ashkenazi Jewish (ASJ) AF: 0.0284 AC: 97 AN: 3412

East Asian (EAS) AF: 0.0377 AC: 187 AN: 4956

South Asian (SAS) AF: 0.0173 AC: 79 AN: 4556

European-Finnish (FIN) AF: 0.0467 AC: 402 AN: 8610

Middle Eastern (MID) AF: 0.0288 AC: 8 AN: 278

European-Non Finnish (NFE) AF: 0.0430 AC: 2846 AN: 66182

Other (OTH) AF: 0.0701 AC: 138 AN: 1970

Alfa AF: 0.0214 Hom.: 121

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs71595363; hg19: chr4-120240802;