rs12061601

Variant names:

• chr1-169101212-T-C
• rs12061601
• ENST00000650631.1:n.131+1934A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-169101212-T-C
• chr1-169101212-T-G

Variant summary

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

The ENST00000650631.1(LINC00970):​n.131+1934A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,128 control chromosomes in the GnomAD database, including 2,214 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 0.16 (2214 hom., cov: 32)
• Consequence: LINC00970 ENST00000650631.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.850
• Publications: 17 publications found

Genes affected

LINC00970 (HGNC:48730): (long intergenic non-protein coding RNA 970)

LINC00970 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00970	ENST00000650631.1	n.131+1934A>G		intron_variant	Intron 1 of 8
LINC00970	ENST00000715524.1	n.131+1934A>G		intron_variant	Intron 1 of 9
LINC00970	ENST00000715525.1	n.132+1934A>G		intron_variant	Intron 1 of 8

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23752 AN: 152010 Hom.: 2213 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0504

Gnomad SAS AF: 0.0628

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.156 AC: 23777 AN: 152128 Hom.: 2214 Cov.: 32 AF XY: 0.154 AC XY: 11468 AN XY: 74386

African (AFR) AF: 0.260 AC: 10771 AN: 41440

American (AMR) AF: 0.118 AC: 1808 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 697 AN: 3468

East Asian (EAS) AF: 0.0503 AC: 260 AN: 5170

South Asian (SAS) AF: 0.0633 AC: 305 AN: 4822

European-Finnish (FIN) AF: 0.123 AC: 1301 AN: 10600

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8173 AN: 68018

Other (OTH) AF: 0.160 AC: 338 AN: 2112

Alfa AF: 0.133 Hom.: 3223

Bravo AF: 0.159

Asia WGS AF: 0.0680 AC: 238 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	0.99
DANN	Benign	0.72
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs12061601; hg19: chr1-169070450;