rs4664406

Positions:

• chr2-161128636-A-G

Variant summary

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

The ENST00000425470.1(TANK-AS1):​n.165+30529T>C 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 0.21 in 152,118 control chromosomes in the GnomAD database, including 3,704 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 0.21 (3704 hom., cov: 32)
• Consequence: TANK-AS1 ENST00000425470.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TANK-AS1	XR_923528.3	n.141+31496T>C		intron_variant, non_coding_transcript_variant
TANK-AS1	XR_923527.2	n.141+31496T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TANK-AS1	ENST00000425470.1	n.165+30529T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31897 AN: 152000 Hom.: 3686 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.210 AC: 31966 AN: 152118 Hom.: 3704 Cov.: 32 AF XY: 0.211 AC XY: 15681 AN XY: 74372

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.179

Alfa AF: 0.206 Hom.: 541

Bravo AF: 0.207

Asia WGS AF: 0.225 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.29
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4664406; hg19: chr2-161985147;