4-119319647-C-CATAATAATA

Variant names:

• chr4-119319647-C-CATAATAATA
• rs71595363
• NM_000134.4:c.241-13_241-5dupTATTATTAT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000134.4(FABP2):​c.241-13_241-5dupTATTATTAT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.22 (3714 hom., cov: 0)
  • Exomes 𝑓: 0.13 (5351 hom.)
  • Failed GnomAD Quality Control
• Consequence: FABP2 NM_000134.4 splice_region, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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 -10 ACMG points.

• BP6: Variant 4-119319647-C-CATAATAATA is Benign according to our data. Variant chr4-119319647-C-CATAATAATA is described in ClinVar as Benign. ClinVar VariationId is 1265548.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

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.241-13_241-5dupTATTATTAT		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_241-4insTATTATTAT		splice_region intron	N/A	ENSP00000274024.3	P12104
	ENSG00000294020	ENST00000720595.1		n.176-14681_176-14680insATAATAATA		intron	N/A
	ENSG00000294020	ENST00000720596.1		n.224-14681_224-14680insATAATAATA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.217 AC: 31339 AN: 144680 Hom.: 3715 Cov.: 0

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.216

GnomAD2 exomes AF: 0.110 AC: 8240 AN: 75038 AF XY: 0.112

Gnomad AFR exome AF: 0.0258

Gnomad AMR exome AF: 0.0474

Gnomad ASJ exome AF: 0.103

Gnomad EAS exome AF: 0.0591

Gnomad FIN exome AF: 0.144

Gnomad NFE exome AF: 0.120

Gnomad OTH exome AF: 0.0986

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.125 AC: 81345 AN: 648982 Hom.: 5351 Cov.: 12 AF XY: 0.129 AC XY: 43232 AN XY: 336088

African (AFR) AF: 0.0775 AC: 978 AN: 12626

American (AMR) AF: 0.107 AC: 1553 AN: 14524

Ashkenazi Jewish (ASJ) AF: 0.0858 AC: 1361 AN: 15866

East Asian (EAS) AF: 0.180 AC: 3988 AN: 22152

South Asian (SAS) AF: 0.0750 AC: 2738 AN: 36492

European-Finnish (FIN) AF: 0.116 AC: 3268 AN: 28150

Middle Eastern (MID) AF: 0.110 AC: 240 AN: 2174

European-Non Finnish (NFE) AF: 0.130 AC: 63599 AN: 487984

Other (OTH) AF: 0.125 AC: 3620 AN: 29014

GnomAD4 genome AF: 0.216 AC: 31324 AN: 144688 Hom.: 3714 Cov.: 0 AF XY: 0.213 AC XY: 14941 AN XY: 70174

African (AFR) AF: 0.144 AC: 5715 AN: 39642

American (AMR) AF: 0.213 AC: 3037 AN: 14282

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 497 AN: 3414

East Asian (EAS) AF: 0.313 AC: 1550 AN: 4952

South Asian (SAS) AF: 0.170 AC: 772 AN: 4546

European-Finnish (FIN) AF: 0.217 AC: 1865 AN: 8590

Middle Eastern (MID) AF: 0.219 AC: 61 AN: 278

European-Non Finnish (NFE) AF: 0.260 AC: 17209 AN: 66130

Other (OTH) AF: 0.217 AC: 428 AN: 1970

Alfa AF: 0.141 Hom.: 121

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

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; COSMIC: COSV56789363;