rs2884364

Variant names:

• chr2-161121136-G-A
• rs2884364
• ENST00000425470.1:n.166-24568C>T

Variant summary

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

The ENST00000425470.1(TANK-AS1):​n.166-24568C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,008 control chromosomes in the GnomAD database, including 10,164 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 0.35 (10164 hom., cov: 32)
• Consequence: TANK-AS1 ENST00000425470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510

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=-0.62).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TANK-AS1	NR_187173.1	n.232-24568C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TANK-AS1	ENST00000425470.1	n.166-24568C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53847 AN: 151890 Hom.: 10158 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.354 AC: 53867 AN: 152008 Hom.: 10164 Cov.: 32 AF XY: 0.355 AC XY: 26378 AN XY: 74290

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.361

Alfa AF: 0.383 Hom.: 23116

Bravo AF: 0.364

Asia WGS AF: 0.398 AC: 1384 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	9.9
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2884364; hg19: chr2-161977647;