NM_016944.2:c.*1748G>A

Variant names:

• chr7-141781136-G-A
• rs17464086
• NM_016944.2:c.*1748G>A

Variant summary

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

The NM_016944.2(TAS2R4):​c.*1748G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,970 control chromosomes in the GnomAD database, including 16,553 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 0.46 (16553 hom., cov: 32)
• Consequence: TAS2R4 NM_016944.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449
• Publications: 10 publications found

Genes affected

TAS2R4 (HGNC:14911): (taste 2 receptor member 4) This gene encodes a member of a family of candidate taste receptors that are members of the G protein-coupled receptor superfamily and that are specifically expressed by taste receptor cells of the tongue and palate epithelia. These apparently intronless genes encode a 7-transmembrane receptor protein, functioning as a bitter taste receptor. This gene is clustered with another 3 candidate taste receptor genes in chromosome 7 and is genetically linked to loci that influence bitter perception. [provided by RefSeq, Jul 2008]

SSBP1 (HGNC:11317): (single stranded DNA binding protein 1) SSBP1 is a housekeeping gene involved in mitochondrial biogenesis (Tiranti et al., 1995 [PubMed 7789991]). It is also a subunit of a single-stranded DNA (ssDNA)-binding complex involved in the maintenance of genome stability (Huang et al., 2009) [PubMed 19683501].[supplied by OMIM, Feb 2010]

SSBP1 Gene-Disease associations (from GenCC):

• optic atrophy 13 with retinal and foveal abnormalities

  Inheritance: AD, AR Classification: STRONG, MODERATE, LIMITED Submitted by: PanelApp Australia, ClinGen, Ambry Genetics
• Leigh syndrome

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016944.2. 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
	TAS2R4	NM_016944.2	MANE Select	c.*1748G>A		3_prime_UTR	Exon 1 of 1	NP_058640.1	Q9NYW5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS2R4	ENST00000247881.4	TSL:6 MANE Select	c.*1748G>A		3_prime_UTR	Exon 1 of 1	ENSP00000247881.3	Q9NYW5
	SSBP1	ENST00000465582.5	TSL:5	c.*31-6587G>A		intron	N/A	ENSP00000420485.1	Q04837

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69322 AN: 151852 Hom.: 16534 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.474

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.457 AC: 69385 AN: 151970 Hom.: 16553 Cov.: 32 AF XY: 0.462 AC XY: 34306 AN XY: 74260

African (AFR) AF: 0.310 AC: 12837 AN: 41432

American (AMR) AF: 0.523 AC: 7998 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1632 AN: 3472

East Asian (EAS) AF: 0.751 AC: 3881 AN: 5168

South Asian (SAS) AF: 0.593 AC: 2847 AN: 4798

European-Finnish (FIN) AF: 0.483 AC: 5098 AN: 10546

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33712 AN: 67960

Other (OTH) AF: 0.478 AC: 1010 AN: 2112

Alfa AF: 0.458 Hom.: 1882

Bravo AF: 0.454

Asia WGS AF: 0.665 AC: 2309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.51
PhyloP100		0.45
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17464086; hg19: chr7-141480936;