chr5-9688168-A-T

Variant names:

• chr5-9688168-A-T
• rs41494
• ENST00000511616.5:n.1344+24004T>A

Variant summary

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

The ENST00000511616.5(LINC02112):​n.1344+24004T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.944 in 152,276 control chromosomes in the GnomAD database, including 68,514 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 0.94 (68514 hom., cov: 32)
• Consequence: LINC02112 ENST00000511616.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 2 publications found

Genes affected

LINC02112 (HGNC:27756): (long intergenic non-protein coding RNA 2112)

TAS2R1 (HGNC:14909): (taste 2 receptor member 1) 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. This intronless taste receptor gene encodes a 7-transmembrane receptor protein, functioning as a bitter taste receptor. This gene is mapped to chromosome 5p15, the location of a genetic locus (PROP) that controls the detection of the bitter compound 6-n-propyl-2-thiouracil. [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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS2R1	NM_001386348.1	c.-242+24004T>A		intron_variant	Intron 8 of 9		NP_001373277.1
LINC02112	NR_027112.2	n.1342+24004T>A		intron_variant	Intron 9 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02112	ENST00000511616.5	n.1344+24004T>A		intron_variant	Intron 9 of 12	1
LINC02112	ENST00000606744.1	n.65+24004T>A		intron_variant	Intron 1 of 2	1
TAS2R1	ENST00000514078.1	c.-81+24004T>A		intron_variant	Intron 1 of 1	3		ENSP00000476190.1
TAS2R1	ENST00000506620.1	c.-242+24004T>A		intron_variant	Intron 1 of 2	2		ENSP00000475387.1

Frequencies

GnomAD3 genomes AF: 0.944 AC: 143694 AN: 152158 Hom.: 68459 Cov.: 32

Gnomad AFR AF: 0.924

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.944 AC: 143811 AN: 152276 Hom.: 68514 Cov.: 32 AF XY: 0.938 AC XY: 69804 AN XY: 74452

African (AFR) AF: 0.924 AC: 38401 AN: 41556

American (AMR) AF: 0.887 AC: 13557 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.983 AC: 3414 AN: 3472

East Asian (EAS) AF: 0.539 AC: 2788 AN: 5168

South Asian (SAS) AF: 0.940 AC: 4529 AN: 4820

European-Finnish (FIN) AF: 0.946 AC: 10048 AN: 10620

Middle Eastern (MID) AF: 0.997 AC: 293 AN: 294

European-Non Finnish (NFE) AF: 0.997 AC: 67857 AN: 68038

Other (OTH) AF: 0.953 AC: 2014 AN: 2114

Alfa AF: 0.973 Hom.: 8957

Bravo AF: 0.937

Asia WGS AF: 0.763 AC: 2655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.086
DANN	Benign	0.43
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs41494; hg19: chr5-9688280;