rs17275322

chr5-9766153-A-Cchr5-9766153-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_027112.2(LINC02112):n.520-460T>G 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 0.0301 in 152,356 control chromosomes in the GnomAD database, including 71 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 0.030 (71 hom., cov: 33)
• Consequence: LINC02112 NR_027112.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364

Genes affected

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

LOC105374649 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0301 (4580/152356) while in subpopulation AFR AF= 0.0334 (1389/41590). AF 95% confidence interval is 0.0321. There are 71 homozygotes in gnomad4. There are 2154 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 71 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02112	NR_027112.2	n.520-460T>G		intron_variant, non_coding_transcript_variant
LOC105374649	XR_925776.2	n.104-9345A>C		intron_variant, non_coding_transcript_variant
TAS2R1	NM_001386348.1	c.-841-51914T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02112	ENST00000511616.5	n.522-460T>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0300 AC: 4571 AN: 152238 Hom.: 71 Cov.: 33

Gnomad AFR AF: 0.0333

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0329

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00559

Gnomad FIN AF: 0.0159

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0333

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0301 AC: 4580 AN: 152356 Hom.: 71 Cov.: 33 AF XY: 0.0289 AC XY: 2154 AN XY: 74494

Gnomad4 AFR AF: 0.0334

Gnomad4 AMR AF: 0.0329

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00559

Gnomad4 FIN AF: 0.0159

Gnomad4 NFE AF: 0.0333

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0232 Hom.: 9

Bravo AF: 0.0319

Asia WGS AF: 0.00606 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	10
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17275322; hg19: chr5-9766265;