rs7725217

Variant names:

• chr5-9756217-A-C
• rs7725217
• ENST00000511616.5:n.744+9254T>G

Variant summary

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

The ENST00000511616.5(LINC02112):​n.744+9254T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,144 control chromosomes in the GnomAD database, including 5,323 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 0.25 (5323 hom., cov: 32)
• Consequence: LINC02112 ENST00000511616.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.815
• Publications: 5 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]

LOC105374649 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS2R1	NM_001386348.1	c.-841-41978T>G		intron_variant	Intron 4 of 9		NP_001373277.1
LINC02112	NR_027112.2	n.742+9254T>G		intron_variant	Intron 5 of 12
LOC105374649	XR_925776.2	n.103+4750A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02112	ENST00000511616.5	n.744+9254T>G		intron_variant	Intron 5 of 12	1

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37780 AN: 152026 Hom.: 5318 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.248 AC: 37789 AN: 152144 Hom.: 5323 Cov.: 32 AF XY: 0.249 AC XY: 18499 AN XY: 74382

African (AFR) AF: 0.126 AC: 5234 AN: 41522

American (AMR) AF: 0.258 AC: 3943 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1470 AN: 3470

East Asian (EAS) AF: 0.223 AC: 1152 AN: 5168

South Asian (SAS) AF: 0.271 AC: 1304 AN: 4816

European-Finnish (FIN) AF: 0.238 AC: 2516 AN: 10578

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21043 AN: 67992

Other (OTH) AF: 0.305 AC: 645 AN: 2112

Alfa AF: 0.277 Hom.: 9987

Bravo AF: 0.242

Asia WGS AF: 0.255 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.53
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs7725217; hg19: chr5-9756329;