rs13245023

Positions:

• chr7-20845476-C-G
• chr7-20845476-C-T

Variant summary

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

The NR_126381.1(LINC01162):​n.74+9972C>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 0.0288 in 152,174 control chromosomes in the GnomAD database, including 87 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 0.029 (87 hom., cov: 32)
• Consequence: LINC01162 NR_126381.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

LINC01162 (HGNC:49528): (long intergenic non-protein coding RNA 1162)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0288 (4387/152174) while in subpopulation SAS AF= 0.0529 (255/4820). AF 95% confidence interval is 0.0476. There are 87 homozygotes in gnomad4. There are 2095 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 87 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01162	NR_126381.1	n.74+9972C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01162	ENST00000661032.1	n.129+9972C>G		intron_variant, non_coding_transcript_variant
LINC01162	ENST00000447262.2	n.74+9972C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0289 AC: 4388 AN: 152056 Hom.: 87 Cov.: 32

Gnomad AFR AF: 0.00720

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0202

Gnomad ASJ AF: 0.0374

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0531

Gnomad FIN AF: 0.0397

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0425

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0288 AC: 4387 AN: 152174 Hom.: 87 Cov.: 32 AF XY: 0.0282 AC XY: 2095 AN XY: 74398

Gnomad4 AFR AF: 0.00718

Gnomad4 AMR AF: 0.0201

Gnomad4 ASJ AF: 0.0374

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0529

Gnomad4 FIN AF: 0.0397

Gnomad4 NFE AF: 0.0425

Gnomad4 OTH AF: 0.0246

Alfa AF: 0.0136 Hom.: 8

Bravo AF: 0.0242

Asia WGS AF: 0.0150 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.12
DANN	Benign	0.49
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13245023; hg19: chr7-20885095;