6-159004675-C-T

Variant names:

• chr6-159004675-C-T
• rs2016588
• ENST00000606470.2:n.29+4765C>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.236+14103C>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 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 ENST00000607391.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 17 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=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.639 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.520+4283C>T		intron	N/A
	TAGAP-AS1	NR_183546.1		n.520+4283C>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+4765C>T		intron	N/A
	TAGAP-AS1	ENST00000607391.5	TSL:3	n.236+14103C>T		intron	N/A
	TAGAP-AS1	ENST00000607796.6	TSL:5	n.29+4765C>T		intron	N/A

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

African (AFR) AF: 0.335 AC: 13871 AN: 41434

American (AMR) AF: 0.493 AC: 7535 AN: 15274

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

East Asian (EAS) AF: 0.501 AC: 2586 AN: 5158

South Asian (SAS) AF: 0.658 AC: 3168 AN: 4814

European-Finnish (FIN) AF: 0.605 AC: 6373 AN: 10526

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

European-Non Finnish (NFE) AF: 0.634 AC: 43110 AN: 67972

Other (OTH) AF: 0.545 AC: 1150 AN: 2110

Alfa AF: 0.597 Hom.: 94781

Bravo AF: 0.508

Asia WGS AF: 0.583 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.8
DANN	Benign	0.82
PhyloP100		0.016

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: rs2016588;

hg19: chr6-159425707;

COSMIC: COSV51921794;