rs1404635

Variant names:

• chr7-143478061-G-A
• rs1404635
• NM_176883.2:c.189G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-143478061-G-A
• chr7-143478061-G-C
• chr7-143478061-G-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_176883.2(TAS2R41):​c.189G>A​(p.Thr63Thr) 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
• Publications: 25 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_176883.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS2R41	NM_176883.2	MANE Select	c.189G>A	p.Thr63Thr	synonymous	Exon 1 of 1	NP_795364.2
	EPHA1-AS1	NR_033897.1		n.207-26713G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS2R41	ENST00000408916.1	TSL:6 MANE Select	c.189G>A	p.Thr63Thr	synonymous	Exon 1 of 1	ENSP00000386201.1
	EPHA1-AS1	ENST00000429289.5	TSL:1	n.207-26713G>A		intron	N/A
	EPHA1-AS1	ENST00000690912.2		n.228-17905G>A		intron	N/A

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

GnomAD2 exomes AF: 0.266 AC: 66240 AN: 249162 AF XY: 0.270

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 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

African (AFR) AF: 0.0504 AC: 1688 AN: 33480

American (AMR) AF: 0.289 AC: 12935 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 6620 AN: 26136

East Asian (EAS) AF: 0.315 AC: 12497 AN: 39700

South Asian (SAS) AF: 0.316 AC: 27299 AN: 86258

European-Finnish (FIN) AF: 0.269 AC: 14366 AN: 53420

Middle Eastern (MID) AF: 0.200 AC: 1152 AN: 5768

European-Non Finnish (NFE) AF: 0.278 AC: 309107 AN: 1111998

Other (OTH) AF: 0.265 AC: 15981 AN: 60396

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

African (AFR) AF: 0.0593 AC: 2459 AN: 41490

American (AMR) AF: 0.282 AC: 4310 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 901 AN: 3466

East Asian (EAS) AF: 0.291 AC: 1497 AN: 5140

South Asian (SAS) AF: 0.321 AC: 1543 AN: 4814

European-Finnish (FIN) AF: 0.266 AC: 2802 AN: 10538

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19052 AN: 67934

Other (OTH) AF: 0.231 AC: 487 AN: 2106

Alfa AF: 0.250 Hom.: 8067

Bravo AF: 0.209

Asia WGS AF: 0.271 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.3
DANN	Benign	0.60
PhyloP100		0.14
PromoterAI		-0.0027	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1404635; hg19: chr7-143175154; COSMIC: COSV68765268;