chr10-93588425-T-C

Position:

• chr10-93588425-T-C

Variant summary

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

The NM_001195755.2(FFAR4):​c.*816T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,152 control chromosomes in the GnomAD database, including 15,513 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 0.43 (15513 hom., cov: 29)
  • Failed GnomAD Quality Control
• Consequence: FFAR4 NM_001195755.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FFAR4	NM_001195755.2	c.*816T>C		3_prime_UTR_variant	3/3	ENST00000371481.9
FFAR4	NM_181745.4	c.*816T>C		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FFAR4	ENST00000371481.9	c.*816T>C		3_prime_UTR_variant	3/3	1	NM_001195755.2	P1
FFAR4	ENST00000371483.8	c.*816T>C		3_prime_UTR_variant	4/4	1
FFAR4	ENST00000604414.1	c.696+12206T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65492 AN: 151034 Hom.: 15475 Cov.: 29

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.436

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.434 AC: 65595 AN: 151152 Hom.: 15513 Cov.: 29 AF XY: 0.433 AC XY: 31948 AN XY: 73802

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.431

Alfa AF: 0.392 Hom.: 16136

Bravo AF: 0.436

Asia WGS AF: 0.281 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.79

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: rs10882272; hg19: chr10-95348182;