chr7-125337682-T-C

Position:

• chr7-125337682-T-C

Variant summary

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

The NR_110188.1(LOC101928283):​n.1007+2267T>C 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 0.188 in 151,964 control chromosomes in the GnomAD database, including 3,068 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 0.19 (3068 hom., cov: 32)
• Consequence: LOC101928283 NR_110188.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.569

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928283	NR_110188.1	n.1007+2267T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POT1-AS1	ENST00000651909.1	n.262-9443T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28560 AN: 151846 Hom.: 3067 Cov.: 32

Gnomad AFR AF: 0.0844

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.188 AC: 28565 AN: 151964 Hom.: 3068 Cov.: 32 AF XY: 0.190 AC XY: 14132 AN XY: 74256

Gnomad4 AFR AF: 0.0842

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.189

Alfa AF: 0.223 Hom.: 5170

Bravo AF: 0.176

Asia WGS AF: 0.179 AC: 623 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.6
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7795867; hg19: chr7-124977736;