6-159019695-C-T

Variant names:

• chr6-159019695-C-T
• rs1973919
• ENST00000606470.2:n.29+19785C>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.237-6254C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,074 control chromosomes in the GnomAD database, including 33,546 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 0.65 (33546 hom., cov: 32)
• Consequence: TAGAP-AS1 ENST00000607391.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 6 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 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.521-6254C>T		intron	N/A
	TAGAP-AS1	NR_183546.1		n.521-6254C>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+19785C>T		intron	N/A
	TAGAP-AS1	ENST00000607391.5	TSL:3	n.237-6254C>T		intron	N/A
	TAGAP-AS1	ENST00000607796.6	TSL:5	n.30-6254C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98456 AN: 151958 Hom.: 33536 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.648 AC: 98492 AN: 152074 Hom.: 33546 Cov.: 32 AF XY: 0.657 AC XY: 48808 AN XY: 74342

African (AFR) AF: 0.420 AC: 17392 AN: 41440

American (AMR) AF: 0.764 AC: 11684 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2600 AN: 3472

East Asian (EAS) AF: 0.906 AC: 4696 AN: 5182

South Asian (SAS) AF: 0.817 AC: 3943 AN: 4824

European-Finnish (FIN) AF: 0.716 AC: 7566 AN: 10564

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48258 AN: 67982

Other (OTH) AF: 0.669 AC: 1412 AN: 2110

Alfa AF: 0.621 Hom.: 3277

Bravo AF: 0.640

Asia WGS AF: 0.842 AC: 2927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.36
PhyloP100		-0.061

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: rs1973919;

hg19: chr6-159440727;