6-159015562-G-T

Position:

• chr6-159015562-G-T

Variant summary

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

The NR_183546.1(TAGAP-AS1):​n.521-10387G>T 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 0.532 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 NR_183546.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAGAP-AS1	NR_183546.1	n.521-10387G>T		intron_variant, non_coding_transcript_variant
TAGAP-AS1	NR_183545.1	n.521-10387G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAGAP-AS1	ENST00000646912.1	n.25+15652G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.545

Alfa AF: 0.570 Hom.: 4374

Bravo AF: 0.508

Asia WGS AF: 0.582 AC: 2025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2057061; hg19: chr6-159436594;