5-9688168-A-T

Position:

• chr5-9688168-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_027112.2(LINC02112):​n.1342+24004T>A variant causes a intron, non coding transcript 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 NR_027112.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02112	NR_027112.2	n.1342+24004T>A		intron_variant, non_coding_transcript_variant
TAS2R1	NM_001386348.1	c.-242+24004T>A		intron_variant			NP_001373277.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02112	ENST00000511616.5	n.1344+24004T>A		intron_variant, non_coding_transcript_variant		1
LINC02112	ENST00000606744.1	n.65+24004T>A		intron_variant, non_coding_transcript_variant		1
TAS2R1	ENST00000506620.1	c.-242+24004T>A		intron_variant		2		ENSP00000475387
TAS2R1	ENST00000514078.1	c.-81+24004T>A		intron_variant		3		ENSP00000476190

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

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.983

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.940

Gnomad4 FIN AF: 0.946

Gnomad4 NFE AF: 0.997

Gnomad4 OTH AF: 0.953

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41494; hg19: chr5-9688280;