chr10-93587718-C-T

Variant names:

• chr10-93587718-C-T
• rs17108973
• NM_001195755.2:c.*109C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001195755.2. 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
	FFAR4	NM_001195755.2	MANE Select	c.*109C>T		3_prime_UTR	Exon 3 of 3	NP_001182684.1	Q5NUL3-2
	FFAR4	NM_181745.4		c.*109C>T		3_prime_UTR	Exon 4 of 4	NP_859529.2	Q5NUL3-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FFAR4	ENST00000371481.9	TSL:1 MANE Select	c.*109C>T		3_prime_UTR	Exon 3 of 3	ENSP00000360536.5	Q5NUL3-2
	FFAR4	ENST00000371483.8	TSL:1	c.*109C>T		3_prime_UTR	Exon 4 of 4	ENSP00000360538.4	Q5NUL3-1
	FFAR4	ENST00000944863.1		c.*109C>T		3_prime_UTR	Exon 2 of 2	ENSP00000614922.1

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

African (AFR) AF: 0.121 AC: 2606 AN: 21504

American (AMR) AF: 0.139 AC: 4069 AN: 29258

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 4131 AN: 17246

East Asian (EAS) AF: 0.106 AC: 3937 AN: 37026

South Asian (SAS) AF: 0.315 AC: 18730 AN: 59420

European-Finnish (FIN) AF: 0.153 AC: 5279 AN: 34464

Middle Eastern (MID) AF: 0.234 AC: 930 AN: 3974

European-Non Finnish (NFE) AF: 0.159 AC: 104053 AN: 654850

Other (OTH) AF: 0.175 AC: 7218 AN: 41236

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

African (AFR) AF: 0.132 AC: 5466 AN: 41454

American (AMR) AF: 0.169 AC: 2574 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 816 AN: 3458

East Asian (EAS) AF: 0.107 AC: 551 AN: 5170

South Asian (SAS) AF: 0.336 AC: 1621 AN: 4818

European-Finnish (FIN) AF: 0.162 AC: 1706 AN: 10548

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11825 AN: 67958

Other (OTH) AF: 0.195 AC: 412 AN: 2112

Alfa AF: 0.165 Hom.: 613

Bravo AF: 0.162

Asia WGS AF: 0.194 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.61
PhyloP100		-0.32
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: rs17108973; hg19: chr10-95347475; COSMIC: COSV65160308; COSMIC: COSV65160308;