rs4664406

Variant names:

• chr2-161128636-A-G
• rs4664406
• ENST00000425470.1:n.165+30529T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000425470.1(TANK-AS1):​n.165+30529T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TANK-AS1	NR_187173.1	n.231+30529T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TANK-AS1	ENST00000425470.1	n.165+30529T>C		intron_variant	Intron 2 of 2	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

African (AFR) AF: 0.292 AC: 12093 AN: 41472

American (AMR) AF: 0.148 AC: 2270 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 447 AN: 3466

East Asian (EAS) AF: 0.215 AC: 1111 AN: 5176

South Asian (SAS) AF: 0.115 AC: 556 AN: 4816

European-Finnish (FIN) AF: 0.251 AC: 2648 AN: 10568

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12377 AN: 68012

Other (OTH) AF: 0.179 AC: 378 AN: 2112

Alfa AF: 0.208 Hom.: 566

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
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs4664406; hg19: chr2-161985147;