7-125325175-C-T

Variant names:

• chr7-125325175-C-T
• rs7810309
• ENST00000424515.2:n.649-4507C>T

Variant summary

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

The ENST00000458437.2(POT1-AS1):​n.269-21950C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0857 in 152,096 control chromosomes in the GnomAD database, including 622 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 0.086 (622 hom., cov: 33)
• Consequence: POT1-AS1 ENST00000458437.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000458437.2. 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.632-4507C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POT1-AS1	ENST00000424515.2	TSL:5	n.649-4507C>T		intron	N/A
	POT1-AS1	ENST00000458437.2	TSL:3	n.269-21950C>T		intron	N/A
	POT1-AS1	ENST00000651909.1		n.262-21950C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0857 AC: 13019 AN: 151978 Hom.: 620 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.0565

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0760

Gnomad OTH AF: 0.0850

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

GnomAD4 genome AF: 0.0857 AC: 13041 AN: 152096 Hom.: 622 Cov.: 33 AF XY: 0.0860 AC XY: 6392 AN XY: 74362

African (AFR) AF: 0.101 AC: 4192 AN: 41482

American (AMR) AF: 0.0564 AC: 862 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0928 AC: 322 AN: 3470

East Asian (EAS) AF: 0.105 AC: 542 AN: 5166

South Asian (SAS) AF: 0.200 AC: 962 AN: 4818

European-Finnish (FIN) AF: 0.0686 AC: 726 AN: 10584

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0760 AC: 5167 AN: 67990

Other (OTH) AF: 0.0875 AC: 184 AN: 2104

Alfa AF: 0.0816 Hom.: 1060

Bravo AF: 0.0832

Asia WGS AF: 0.174 AC: 606 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.35
PhyloP100		1.1

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: rs7810309;

hg19: chr7-124965229;