2-161131972-T-C

Variant names:

• chr2-161131972-T-C
• rs1267070
• ENST00000425470.1:n.165+27193A>G

Variant summary

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

The ENST00000425470.1(TANK-AS1):​n.165+27193A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,160 control chromosomes in the GnomAD database, including 50,233 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 0.81 (50233 hom., cov: 32)
• Consequence: TANK-AS1 ENST00000425470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 12 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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.231+27193A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TANK-AS1	ENST00000425470.1	TSL:3	n.165+27193A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123293 AN: 152042 Hom.: 50183 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.811 AC: 123399 AN: 152160 Hom.: 50233 Cov.: 32 AF XY: 0.815 AC XY: 60660 AN XY: 74388

African (AFR) AF: 0.753 AC: 31266 AN: 41514

American (AMR) AF: 0.862 AC: 13182 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2772 AN: 3468

East Asian (EAS) AF: 0.996 AC: 5158 AN: 5180

South Asian (SAS) AF: 0.852 AC: 4110 AN: 4822

European-Finnish (FIN) AF: 0.801 AC: 8461 AN: 10568

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.822 AC: 55885 AN: 67992

Other (OTH) AF: 0.809 AC: 1711 AN: 2114

Alfa AF: 0.825 Hom.: 25566

Bravo AF: 0.815

Asia WGS AF: 0.915 AC: 3179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.67
DANN	Benign	0.48
PhyloP100		-0.24

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: rs1267070;

hg19: chr2-161988483;