rs9332427

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POT1-AS1	NR_125718.1	n.145-3376C>T		intron_variant	Intron 1 of 10
POT1-AS1	NR_125719.1	n.145-3376C>T		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POT1-AS1	ENST00000449642.5	n.103-3376C>T		intron_variant	Intron 1 of 7	1
POT1-AS1	ENST00000453342.5	n.97-3376C>T		intron_variant	Intron 1 of 10	1
POT1-AS1	ENST00000429134.5	n.145-3376C>T		intron_variant	Intron 1 of 4	4

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

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.576

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.574

Alfa AF: 0.604 Hom.: 3490

Bravo AF: 0.597

Asia WGS AF: 0.602 AC: 2094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332427; hg19: chr7-124576958;