rs7586242

chr2-161131589-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000425470.1(TANK-AS1):n.165+27576G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TANK-AS1	XR_923528.3	n.141+28543G>A		intron_variant, non_coding_transcript_variant
TANK-AS1	XR_923527.2	n.141+28543G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TANK-AS1	ENST00000425470.1	n.165+27576G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.0888

Gnomad4 ASJ AF: 0.0695

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.0872

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.0453

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0827 Hom.: 191

Bravo AF: 0.126

Asia WGS AF: 0.203 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.3
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7586242; hg19: chr2-161988100;