chr7-125325175-C-T

Position:

• chr7-125325175-C-T

Variant summary

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

The NR_110188.1(LOC101928283):​n.632-4507C>T variant causes a intron, non coding transcript 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: LOC101928283 NR_110188.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928283	NR_110188.1	n.632-4507C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POT1-AS1	ENST00000651909.1	n.262-21950C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0564

Gnomad4 ASJ AF: 0.0928

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.0686

Gnomad4 NFE AF: 0.0760

Gnomad4 OTH AF: 0.0875

Alfa AF: 0.0855 Hom.: 306

Bravo AF: 0.0832

Asia WGS AF: 0.174 AC: 606 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7810309; hg19: chr7-124965229;