rs7586242

Variant names:

• chr2-161131589-C-T
• rs7586242
• ENST00000425470.1:n.165+27576G>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.165+27576G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,140 control chromosomes in the GnomAD database, including 1,865 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 0.12 (1865 hom., cov: 32)
• Consequence: TANK-AS1 ENST00000425470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 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+27576G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TANK-AS1	ENST00000425470.1	TSL:3	n.165+27576G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18633 AN: 152020 Hom.: 1847 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0887

Gnomad ASJ AF: 0.0695

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.0870

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0453

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.123 AC: 18705 AN: 152140 Hom.: 1865 Cov.: 32 AF XY: 0.126 AC XY: 9368 AN XY: 74370

African (AFR) AF: 0.261 AC: 10827 AN: 41476

American (AMR) AF: 0.0888 AC: 1359 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0695 AC: 241 AN: 3470

East Asian (EAS) AF: 0.199 AC: 1030 AN: 5168

South Asian (SAS) AF: 0.0872 AC: 421 AN: 4826

European-Finnish (FIN) AF: 0.144 AC: 1519 AN: 10574

Middle Eastern (MID) AF: 0.0342 AC: 10 AN: 292

European-Non Finnish (NFE) AF: 0.0453 AC: 3080 AN: 68014

Other (OTH) AF: 0.102 AC: 215 AN: 2110

Alfa AF: 0.0680 Hom.: 936

Bravo AF: 0.126

Asia WGS AF: 0.203 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.39
PhyloP100		0.15

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: rs7586242;

hg19: chr2-161988100;