chr10-93587718-C-T

Position:

• chr10-93587718-C-T

Variant summary

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

The NM_001195755.2(FFAR4):​c.*109C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 1,050,978 control chromosomes in the GnomAD database, including 16,312 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 0.17 (2213 hom., cov: 31)
  • Exomes 𝑓: 0.17 (14099 hom.)
• Consequence: FFAR4 NM_001195755.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FFAR4	NM_001195755.2	c.*109C>T		3_prime_UTR_variant	3/3	ENST00000371481.9	NP_001182684.1
FFAR4	NM_181745.4	c.*109C>T		3_prime_UTR_variant	4/4		NP_859529.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FFAR4	ENST00000371481.9	c.*109C>T		3_prime_UTR_variant	3/3	1	NM_001195755.2	ENSP00000360536.5
FFAR4	ENST00000371483.8	c.*109C>T		3_prime_UTR_variant	4/4	1		ENSP00000360538.4
FFAR4	ENST00000604414.1	c.696+11499C>T		intron_variant		3		ENSP00000474477.1

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25072 AN: 151882 Hom.: 2215 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.197

GnomAD4 exome AF: 0.168 AC: 150953 AN: 898978 Hom.: 14099 Cov.: 12 AF XY: 0.174 AC XY: 79874 AN XY: 458368

Gnomad4 AFR exome AF: 0.121

Gnomad4 AMR exome AF: 0.139

Gnomad4 ASJ exome AF: 0.240

Gnomad4 EAS exome AF: 0.106

Gnomad4 SAS exome AF: 0.315

Gnomad4 FIN exome AF: 0.153

Gnomad4 NFE exome AF: 0.159

Gnomad4 OTH exome AF: 0.175

GnomAD4 genome AF: 0.165 AC: 25101 AN: 152000 Hom.: 2213 Cov.: 31 AF XY: 0.169 AC XY: 12573 AN XY: 74284

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.195

Alfa AF: 0.160 Hom.: 277

Bravo AF: 0.162

Asia WGS AF: 0.194 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.61

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

Publications

LitVar

Other links and lift over

dbSNP: rs17108973; hg19: chr10-95347475; COSMIC: COSV65160308; COSMIC: COSV65160308;