rs13245023

Variant names:

• chr7-20845476-C-G
• rs13245023
• ENST00000447262.2:n.74+9972C>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000447262.2(LINC01162):​n.74+9972C>G variant causes a intron 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 ENST00000447262.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 87 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01162	NR_126381.1	n.74+9972C>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01162	ENST00000447262.2	n.74+9972C>G		intron_variant	Intron 1 of 5	5
LINC01162	ENST00000661032.1	n.129+9972C>G		intron_variant	Intron 1 of 8
LINC01162	ENST00000742942.1	n.179+9972C>G		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.00718 AC: 298 AN: 41506

American (AMR) AF: 0.0201 AC: 308 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0374 AC: 130 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0529 AC: 255 AN: 4820

European-Finnish (FIN) AF: 0.0397 AC: 420 AN: 10574

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0425 AC: 2888 AN: 68016

Other (OTH) AF: 0.0246 AC: 52 AN: 2112

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
PhyloP100		-1.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs13245023; hg19: chr7-20885095;