6-159015562-G-T

Variant names:

• chr6-159015562-G-T
• rs2057061
• ENST00000606470.2:n.29+15652G>T

Variant summary

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

The ENST00000607391.5(TAGAP-AS1):​n.237-10387G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,024 control chromosomes in the GnomAD database, including 22,832 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 0.53 (22832 hom., cov: 32)
• Consequence: TAGAP-AS1 ENST00000607391.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 5 publications found

Genes affected

TAGAP-AS1 (HGNC:55239): (TAGAP antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607391.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAGAP-AS1	NR_183545.1		n.521-10387G>T		intron	N/A
	TAGAP-AS1	NR_183546.1		n.521-10387G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAGAP-AS1	ENST00000606470.2	TSL:5	n.29+15652G>T		intron	N/A
	TAGAP-AS1	ENST00000607391.5	TSL:3	n.237-10387G>T		intron	N/A
	TAGAP-AS1	ENST00000607796.6	TSL:5	n.30-10387G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80848 AN: 151906 Hom.: 22836 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.532 AC: 80862 AN: 152024 Hom.: 22832 Cov.: 32 AF XY: 0.534 AC XY: 39703 AN XY: 74318

African (AFR) AF: 0.333 AC: 13811 AN: 41422

American (AMR) AF: 0.494 AC: 7550 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2317 AN: 3470

East Asian (EAS) AF: 0.501 AC: 2590 AN: 5172

South Asian (SAS) AF: 0.658 AC: 3163 AN: 4810

European-Finnish (FIN) AF: 0.605 AC: 6395 AN: 10576

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43084 AN: 67974

Other (OTH) AF: 0.545 AC: 1151 AN: 2112

Alfa AF: 0.563 Hom.: 4417

Bravo AF: 0.508

Asia WGS AF: 0.582 AC: 2025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		0.20

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2057061;

hg19: chr6-159436594;