7-143478081-C-T

Variant names:

• chr7-143478081-C-T
• rs935664838
• NM_176883.2:c.209C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_176883.2(TAS2R41):​c.209C>T​(p.Ser70Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S70Y) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: TAS2R41 NM_176883.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.03321719).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS2R41	NM_176883.2	MANE Select	c.209C>T	p.Ser70Phe	missense	Exon 1 of 1	NP_795364.2	P59536
	EPHA1-AS1	NR_033897.1		n.207-26693C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS2R41	ENST00000408916.1	TSL:6 MANE Select	c.209C>T	p.Ser70Phe	missense	Exon 1 of 1	ENSP00000386201.1	P59536
	EPHA1-AS1	ENST00000429289.5	TSL:1	n.207-26693C>T		intron	N/A
	EPHA1-AS1	ENST00000690912.2		n.228-17885C>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 44

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.073
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.67
CADD	Benign	0.035
DANN	Benign	0.52
DEOGEN2	Benign	0.00041	T
Eigen	Benign	-1.7
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.0013	N
M_CAP	Benign	0.0073	T
MetaRNN	Benign	0.033	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.69	N
PhyloP100		-0.45
PrimateAI	Benign	0.23	T
PROVEAN	Benign	3.2	N
REVEL	Benign	0.033
Sift	Benign	1.0	T
Sift4G	Benign	1.0	T
Polyphen		0.0010	B
Vest4		0.14
MutPred		0.57		Loss of disorder (P = 0.0137)
MVP		0.20
MPC		0.058
ClinPred		0.059	T
GERP RS		-3.6
PromoterAI		0.0036	Neutral
Varity_R		0.031
gMVP		0.15
Mutation Taster		=93/7	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs935664838; hg19: chr7-143175174;