rs6822469

Variant names:

• chr4-16256054-T-C
• rs6822469
• ENST00000570786.1:n.235-203T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000573308.5(TAPT1-AS1):​n.595-254T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,942 control chromosomes in the GnomAD database, including 7,669 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 0.31 (7669 hom., cov: 31)
• Consequence: TAPT1-AS1 ENST00000573308.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499
• Publications: 3 publications found

Genes affected

TAPT1-AS1 (HGNC:26832): (TAPT1 antisense RNA 1 (head to head))

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000573308.5. 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
	TAPT1-AS1	NR_027696.1		n.617-203T>C		intron	N/A
	TAPT1-AS1	NR_027697.1		n.617-254T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAPT1-AS1	ENST00000570786.1	TSL:5	n.235-203T>C		intron	N/A
	TAPT1-AS1	ENST00000573308.5	TSL:2	n.595-254T>C		intron	N/A
	TAPT1-AS1	ENST00000573950.5	TSL:3	n.272+17183T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46845 AN: 151822 Hom.: 7657 Cov.: 31

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.309 AC: 46900 AN: 151942 Hom.: 7669 Cov.: 31 AF XY: 0.306 AC XY: 22741 AN XY: 74264

African (AFR) AF: 0.416 AC: 17233 AN: 41426

American (AMR) AF: 0.281 AC: 4286 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1131 AN: 3460

East Asian (EAS) AF: 0.452 AC: 2333 AN: 5164

South Asian (SAS) AF: 0.231 AC: 1118 AN: 4832

European-Finnish (FIN) AF: 0.254 AC: 2685 AN: 10558

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17194 AN: 67922

Other (OTH) AF: 0.305 AC: 644 AN: 2112

Alfa AF: 0.274 Hom.: 25109

Bravo AF: 0.320

Asia WGS AF: 0.362 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.1
DANN	Benign	0.47
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs6822469; hg19: chr4-16257677;