rs1559971

Variant names:

• chr7-125322031-T-C
• rs1559971
• ENST00000424515.2:n.649-7651T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-125322031-T-C
• chr7-125322031-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000458437.2(POT1-AS1):​n.269-25094T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,926 control chromosomes in the GnomAD database, including 7,034 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 0.30 (7034 hom., cov: 32)
• Consequence: POT1-AS1 ENST00000458437.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.836

Genes affected

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

LOC101928283 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928283	NR_110188.1	n.632-7651T>C		intron_variant	Intron 3 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POT1-AS1	ENST00000424515.2	n.649-7651T>C		intron_variant	Intron 4 of 9	5
POT1-AS1	ENST00000458437.2	n.269-25094T>C		intron_variant	Intron 3 of 10	3
POT1-AS1	ENST00000651909.1	n.262-25094T>C		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45599 AN: 151808 Hom.: 7023 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.300 AC: 45644 AN: 151926 Hom.: 7034 Cov.: 32 AF XY: 0.302 AC XY: 22455 AN XY: 74264

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.293

Alfa AF: 0.311 Hom.: 3812

Bravo AF: 0.289

Asia WGS AF: 0.358 AC: 1244 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1559971; hg19: chr7-124962085;