7-143444382-T-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_177437.1(TAS2R60):c.930T>C(p.Arg310=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 1,606,254 control chromosomes in the GnomAD database, including 376,327 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 0.65 (33087 hom., cov: 30)
  • Exomes 𝑓: 0.68 (343240 hom.)
• Consequence: TAS2R60 NM_177437.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

Genes affected

TAS2R60 (HGNC:20639): (taste 2 receptor member 60) This gene encodes a member of the bitter taste receptor family which belong to the G protein-coupled receptor superfamily and are predominantly expressed in taste receptor cells of the tongue and palate epithelia. This intronless taste receptor gene encodes a seven-transmembrane receptor protein, functioning as a bitter taste receptor. This gene is clustered together with eight other taste receptor genes on chromosome 7. [provided by RefSeq, Jul 2017]

EPHA1-AS1 (HGNC:27799): (EPHA1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP7: Synonymous conserved (PhyloP=-1.58 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAS2R60	NM_177437.1	c.930T>C	p.Arg310=	synonymous_variant	1/1	ENST00000332690.1
EPHA1-AS1	NR_033897.1	n.206+29183T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAS2R60	ENST00000332690.1	c.930T>C	p.Arg310=	synonymous_variant	1/1		NM_177437.1	P1
EPHA1-AS1	ENST00000429289.5	n.206+29183T>C		intron_variant, non_coding_transcript_variant		1
EPHA1-AS1	ENST00000690912.1	n.227+29183T>C		intron_variant, non_coding_transcript_variant
EPHA1-AS1	ENST00000703017.1	n.205+29183T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99176 AN: 151830 Hom.: 33062 Cov.: 30

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.655

GnomAD3 exomes AF: 0.705 AC: 173606 AN: 246260 Hom.: 62505 AF XY: 0.704 AC XY: 93983 AN XY: 133464

Gnomad AFR exome AF: 0.543

Gnomad AMR exome AF: 0.841

Gnomad ASJ exome AF: 0.599

Gnomad EAS exome AF: 0.870

Gnomad SAS exome AF: 0.751

Gnomad FIN exome AF: 0.655

Gnomad NFE exome AF: 0.665

Gnomad OTH exome AF: 0.693

GnomAD4 exome AF: 0.684 AC: 995033 AN: 1454306 Hom.: 343240 Cov.: 48 AF XY: 0.686 AC XY: 496250 AN XY: 723660

Gnomad4 AFR exome AF: 0.538

Gnomad4 AMR exome AF: 0.831

Gnomad4 ASJ exome AF: 0.598

Gnomad4 EAS exome AF: 0.892

Gnomad4 SAS exome AF: 0.749

Gnomad4 FIN exome AF: 0.663

Gnomad4 NFE exome AF: 0.674

Gnomad4 OTH exome AF: 0.680

GnomAD4 genome AF: 0.653 AC: 99250 AN: 151948 Hom.: 33087 Cov.: 30 AF XY: 0.658 AC XY: 48816 AN XY: 74242

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.875

Gnomad4 SAS AF: 0.773

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.655

Alfa AF: 0.667 Hom.: 48424

Bravo AF: 0.656

Asia WGS AF: 0.775 AC: 2693 AN: 3478

EpiCase AF: 0.661

EpiControl AF: 0.657

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.76
Dann	Benign	0.45

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: rs4595035; hg19: chr7-143141475; COSMIC: COSV60331621;