rs9332427

Variant names:

• chr7-124936904-C-T
• rs9332427
• ENST00000449642.5:n.103-3376C>T

Variant summary

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

The ENST00000449642.5(POT1-AS1):​n.103-3376C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,090 control chromosomes in the GnomAD database, including 26,923 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 0.60 (26923 hom., cov: 32)
• Consequence: POT1-AS1 ENST00000449642.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• Publications: 5 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449642.5. 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
	POT1-AS1	NR_125718.1		n.145-3376C>T		intron	N/A
	POT1-AS1	NR_125719.1		n.145-3376C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POT1-AS1	ENST00000449642.5	TSL:1	n.103-3376C>T		intron	N/A
	POT1-AS1	ENST00000453342.5	TSL:1	n.97-3376C>T		intron	N/A
	POT1-AS1	ENST00000429134.5	TSL:4	n.145-3376C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90439 AN: 151972 Hom.: 26903 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.595 AC: 90504 AN: 152090 Hom.: 26923 Cov.: 32 AF XY: 0.593 AC XY: 44110 AN XY: 74352

African (AFR) AF: 0.624 AC: 25872 AN: 41474

American (AMR) AF: 0.568 AC: 8684 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2033 AN: 3472

East Asian (EAS) AF: 0.576 AC: 2980 AN: 5174

South Asian (SAS) AF: 0.620 AC: 2990 AN: 4824

European-Finnish (FIN) AF: 0.513 AC: 5421 AN: 10564

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40713 AN: 67986

Other (OTH) AF: 0.574 AC: 1211 AN: 2108

Alfa AF: 0.606 Hom.: 3658

Bravo AF: 0.597

Asia WGS AF: 0.602 AC: 2094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
DANN	Benign	0.51
PhyloP100		-0.34

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: rs9332427;

hg19: chr7-124576958;