2-161123371-C-T

Position:

• chr2-161123371-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.166-26803G>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 0.601 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.533

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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TANK-AS1	XR_923528.3	n.141+36761G>A		intron_variant, non_coding_transcript_variant
TANK-AS1	XR_923527.2	n.142-26803G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TANK-AS1	ENST00000425470.1	n.166-26803G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.626

Alfa AF: 0.639 Hom.: 5392

Bravo AF: 0.606

Asia WGS AF: 0.684 AC: 2380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1267082; hg19: chr2-161979882;