chr6-159003923-T-C

Variant names:

• chr6-159003923-T-C
• rs10484916
• ENST00000606470.2:n.29+4013T>C

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+13351T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0827 in 152,266 control chromosomes in the GnomAD database, including 1,258 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 0.083 (1258 hom., cov: 32)
• Consequence: TAGAP-AS1 ENST00000607391.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253
• Publications: 7 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 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+3531T>C		intron	N/A
	TAGAP-AS1	NR_183546.1		n.520+3531T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAGAP-AS1	ENST00000606470.2	TSL:5	n.29+4013T>C		intron	N/A
	TAGAP-AS1	ENST00000607391.5	TSL:3	n.236+13351T>C		intron	N/A
	TAGAP-AS1	ENST00000607796.6	TSL:5	n.29+4013T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0826 AC: 12570 AN: 152148 Hom.: 1255 Cov.: 32

Gnomad AFR AF: 0.0217

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0530

Gnomad OTH AF: 0.0952

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

GnomAD4 genome AF: 0.0827 AC: 12589 AN: 152266 Hom.: 1258 Cov.: 32 AF XY: 0.0902 AC XY: 6719 AN XY: 74456

African (AFR) AF: 0.0218 AC: 906 AN: 41580

American (AMR) AF: 0.244 AC: 3732 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3468

East Asian (EAS) AF: 0.403 AC: 2081 AN: 5162

South Asian (SAS) AF: 0.152 AC: 734 AN: 4828

European-Finnish (FIN) AF: 0.0961 AC: 1019 AN: 10606

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0530 AC: 3605 AN: 68022

Other (OTH) AF: 0.101 AC: 213 AN: 2112

Alfa AF: 0.0643 Hom.: 284

Bravo AF: 0.0970

Asia WGS AF: 0.250 AC: 870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.8
DANN	Benign	0.61
PhyloP100		0.25

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: rs10484916;

hg19: chr6-159424955;