ENST00000424515.2:n.1024+2267T>C

Variant names:

• chr7-125337682-T-C
• rs7795867
• ENST00000424515.2:n.1024+2267T>C

Variant summary

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

The ENST00000424515.2(POT1-AS1):​n.1024+2267T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 151,964 control chromosomes in the GnomAD database, including 3,068 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 0.19 (3068 hom., cov: 32)
• Consequence: POT1-AS1 ENST00000424515.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.569
• Publications: 0 publications found

Genes affected

POT1-AS1 (HGNC:49459): (POT1 antisense RNA 1)

LOC101928283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424515.2. 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
	LOC101928283	NR_110188.1		n.1007+2267T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POT1-AS1	ENST00000424515.2	TSL:5	n.1024+2267T>C		intron	N/A
	POT1-AS1	ENST00000458437.2	TSL:3	n.269-9443T>C		intron	N/A
	POT1-AS1	ENST00000651909.1		n.262-9443T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28560 AN: 151846 Hom.: 3067 Cov.: 32

Gnomad AFR AF: 0.0844

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.188 AC: 28565 AN: 151964 Hom.: 3068 Cov.: 32 AF XY: 0.190 AC XY: 14132 AN XY: 74256

African (AFR) AF: 0.0842 AC: 3497 AN: 41520

American (AMR) AF: 0.194 AC: 2962 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3466

East Asian (EAS) AF: 0.152 AC: 784 AN: 5174

South Asian (SAS) AF: 0.187 AC: 901 AN: 4822

European-Finnish (FIN) AF: 0.288 AC: 3041 AN: 10570

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15878 AN: 67832

Other (OTH) AF: 0.189 AC: 397 AN: 2106

Alfa AF: 0.218 Hom.: 6348

Bravo AF: 0.176

Asia WGS AF: 0.179 AC: 623 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.6
DANN	Benign	0.90
PhyloP100		0.57

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: rs7795867;

hg19: chr7-124977736;