rs1267082

Variant names:

• chr2-161123371-C-T
• rs1267082
• ENST00000425470.1:n.166-26803G>A

Variant summary

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

The ENST00000425470.1(TANK-AS1):​n.166-26803G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 152,024 control chromosomes in the GnomAD database, including 28,786 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 0.60 (28786 hom., cov: 32)
• Consequence: TANK-AS1 ENST00000425470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.533
• Publications: 7 publications found

Genes affected

TANK-AS1 (HGNC:40575): (TANK antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425470.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TANK-AS1	NR_187173.1		n.232-26803G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TANK-AS1	ENST00000425470.1	TSL:3	n.166-26803G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.602 AC: 91398 AN: 151906 Hom.: 28787 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.601 AC: 91425 AN: 152024 Hom.: 28786 Cov.: 32 AF XY: 0.602 AC XY: 44740 AN XY: 74302

African (AFR) AF: 0.403 AC: 16678 AN: 41422

American (AMR) AF: 0.719 AC: 10978 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2228 AN: 3470

East Asian (EAS) AF: 0.780 AC: 4038 AN: 5174

South Asian (SAS) AF: 0.725 AC: 3501 AN: 4828

European-Finnish (FIN) AF: 0.557 AC: 5872 AN: 10542

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45991 AN: 68002

Other (OTH) AF: 0.626 AC: 1323 AN: 2112

Alfa AF: 0.632 Hom.: 5452

Bravo AF: 0.606

Asia WGS AF: 0.684 AC: 2380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	12
DANN	Benign	0.69
PhyloP100		0.53

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1267082;

hg19: chr2-161979882;