7-141790307-A-G

Variant names:

• chr7-141790307-A-G
• rs2234012
• NM_018980.3:c.-55A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018980.3(TAS2R5):​c.-55A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 1,556,620 control chromosomes in the GnomAD database, including 185,043 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 (15220 hom., cov: 32)
  • Exomes 𝑓: 0.49 (169823 hom.)
• Consequence: TAS2R5 NM_018980.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 25 publications found

Genes affected

TAS2R5 (HGNC:14912): (taste 2 receptor member 5) This gene encodes a bitter taste receptor; bitter taste receptors are members of the G protein-coupled receptor superfamily and are specifically expressed by taste receptor cells of the tongue and palate epithelia. Each of these apparently intronless taste receptor genes encodes a 7-transmembrane receptor protein, functioning as a bitter taste receptor. This gene is clustered with another 3 candidate taste receptor genes on chromosome 7 and is genetically linked to loci that influence bitter perception. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018980.3. 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
	TAS2R5	NM_018980.3	MANE Select	c.-55A>G		5_prime_UTR	Exon 1 of 1	NP_061853.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS2R5	ENST00000247883.5	TSL:6 MANE Select	c.-55A>G		5_prime_UTR	Exon 1 of 1	ENSP00000247883.4

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66031 AN: 151932 Hom.: 15209 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.458

GnomAD4 exome AF: 0.489 AC: 686612 AN: 1404570 Hom.: 169823 Cov.: 29 AF XY: 0.490 AC XY: 340610 AN XY: 695590

African (AFR) AF: 0.258 AC: 8028 AN: 31166

American (AMR) AF: 0.538 AC: 19351 AN: 35938

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 10405 AN: 22484

East Asian (EAS) AF: 0.715 AC: 28149 AN: 39370

South Asian (SAS) AF: 0.456 AC: 35138 AN: 77070

European-Finnish (FIN) AF: 0.461 AC: 23253 AN: 50446

Middle Eastern (MID) AF: 0.487 AC: 2219 AN: 4558

European-Non Finnish (NFE) AF: 0.490 AC: 531568 AN: 1085632

Other (OTH) AF: 0.492 AC: 28501 AN: 57906

GnomAD4 genome AF: 0.435 AC: 66080 AN: 152050 Hom.: 15220 Cov.: 32 AF XY: 0.438 AC XY: 32519 AN XY: 74326

African (AFR) AF: 0.265 AC: 11008 AN: 41464

American (AMR) AF: 0.516 AC: 7893 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1632 AN: 3470

East Asian (EAS) AF: 0.715 AC: 3691 AN: 5162

South Asian (SAS) AF: 0.441 AC: 2123 AN: 4810

European-Finnish (FIN) AF: 0.462 AC: 4884 AN: 10572

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33500 AN: 67966

Other (OTH) AF: 0.463 AC: 978 AN: 2112

Alfa AF: 0.482 Hom.: 23171

Bravo AF: 0.435

Asia WGS AF: 0.562 AC: 1953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.37
DANN	Benign	0.35
PhyloP100		-0.16
PromoterAI		-0.0055	Neutral
Mutation Taster		=300/0	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: rs2234012; hg19: chr7-141490107; COSMIC: COSV56094729; COSMIC: COSV56094729;