2-161131972-T-C

Position:

• chr2-161131972-T-C

Variant summary

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

The ENST00000425470.1(TANK-AS1):​n.165+27193A>G 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 0.811 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TANK-AS1	XR_923528.3	n.141+28160A>G		intron_variant, non_coding_transcript_variant
TANK-AS1	XR_923527.2	n.141+28160A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TANK-AS1	ENST00000425470.1	n.165+27193A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.862

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.852

Gnomad4 FIN AF: 0.801

Gnomad4 NFE AF: 0.822

Gnomad4 OTH AF: 0.809

Alfa AF: 0.826 Hom.: 22989

Bravo AF: 0.815

Asia WGS AF: 0.915 AC: 3179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1267070; hg19: chr2-161988483;