rs2016588

Positions:

• chr6-159004675-C-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.520+4283C>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 151,964 control chromosomes in the GnomAD database, including 22,858 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 (22858 hom., cov: 32)
• Consequence: TAGAP-AS1 NR_183546.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

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=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAGAP-AS1	NR_183546.1	n.520+4283C>T		intron_variant, non_coding_transcript_variant
TAGAP-AS1	NR_183545.1	n.520+4283C>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+4765C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80896 AN: 151846 Hom.: 22862 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.658

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: 80911 AN: 151964 Hom.: 22858 Cov.: 32 AF XY: 0.535 AC XY: 39715 AN XY: 74258

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.493

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: 0.616 Hom.: 67363

Bravo AF: 0.508

Asia WGS AF: 0.583 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2016588; hg19: chr6-159425707; COSMIC: COSV51921794;