rs1404635

chr7-143478061-G-Achr7-143478061-G-C

Variant summary

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

The NM_176883.2(TAS2R41):c.189G>A(p.Thr63=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 1,613,844 control chromosomes in the GnomAD database, including 60,774 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 0.22 (4429 hom., cov: 31)
  • Exomes 𝑓: 0.27 (56345 hom.)
• Consequence: TAS2R41 NM_176883.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143

Genes affected

TAS2R41 (HGNC:18883): (taste 2 receptor member 41) 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. Chloramphenicol is an agonist for the encoded protein. [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=-0.74).
• BP7: Synonymous conserved (PhyloP=0.143 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAS2R41	NM_176883.2	c.189G>A	p.Thr63=	synonymous_variant	1/1	ENST00000408916.1
EPHA1-AS1	NR_033897.1	n.207-26713G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAS2R41	ENST00000408916.1	c.189G>A	p.Thr63=	synonymous_variant	1/1		NM_176883.2	P1
EPHA1-AS1	ENST00000429289.5	n.207-26713G>A		intron_variant, non_coding_transcript_variant		1
EPHA1-AS1	ENST00000690912.1	n.228-17905G>A		intron_variant, non_coding_transcript_variant
EPHA1-AS1	ENST00000703017.1	n.206-17905G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33214 AN: 151846 Hom.: 4420 Cov.: 31

Gnomad AFR AF: 0.0594

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.232

GnomAD3 exomes AF: 0.266 AC: 66240 AN: 249162 Hom.: 9242 AF XY: 0.270 AC XY: 36547 AN XY: 135182

Gnomad AFR exome AF: 0.0555

Gnomad AMR exome AF: 0.290

Gnomad ASJ exome AF: 0.254

Gnomad EAS exome AF: 0.274

Gnomad SAS exome AF: 0.320

Gnomad FIN exome AF: 0.272

Gnomad NFE exome AF: 0.272

Gnomad OTH exome AF: 0.259

GnomAD4 exome AF: 0.275 AC: 401645 AN: 1461880 Hom.: 56345 Cov.: 48 AF XY: 0.277 AC XY: 201104 AN XY: 727240

Gnomad4 AFR exome AF: 0.0504

Gnomad4 AMR exome AF: 0.289

Gnomad4 ASJ exome AF: 0.253

Gnomad4 EAS exome AF: 0.315

Gnomad4 SAS exome AF: 0.316

Gnomad4 FIN exome AF: 0.269

Gnomad4 NFE exome AF: 0.278

Gnomad4 OTH exome AF: 0.265

GnomAD4 genome AF: 0.219 AC: 33232 AN: 151964 Hom.: 4429 Cov.: 31 AF XY: 0.223 AC XY: 16531 AN XY: 74260

Gnomad4 AFR AF: 0.0593

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.231

Alfa AF: 0.254 Hom.: 6633

Bravo AF: 0.209

Asia WGS AF: 0.271 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	4.3
Dann	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1404635; hg19: chr7-143175154; COSMIC: COSV68765268;