10-93602293-T-G

Variant names:

• chr10-93602293-T-G
• rs3758538
• ENST00000604414.1:c.697-1781T>G

Variant summary

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

The ENST00000604414.1(FFAR4):​c.697-1781T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,106 control chromosomes in the GnomAD database, including 2,837 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 0.18 (2837 hom., cov: 33)
• Consequence: FFAR4 ENST00000604414.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.864

Genes affected

FFAR4 (HGNC:19061): (free fatty acid receptor 4) This gene encodes a G protein-coupled receptor (GPR) which belongs to the rhodopsin family of GPRs. The encoded protein functions as a receptor for free fatty acids, including omega-3, and participates in suppressing anti-inflammatory responses and insulin sensitizing. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FFAR4	ENST00000604414.1	c.697-1781T>G		intron_variant	Intron 2 of 2	3		ENSP00000474477.1

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27700 AN: 151988 Hom.: 2828 Cov.: 33

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0632

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0939

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.172

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.182 AC: 27734 AN: 152106 Hom.: 2837 Cov.: 33 AF XY: 0.177 AC XY: 13163 AN XY: 74360

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.0628

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.0939

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.172

Alfa AF: 0.162 Hom.: 2816

Bravo AF: 0.189

Asia WGS AF: 0.131 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.2
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3758538; hg19: chr10-95362050;