8-126769195-T-G

Position:

• chr8-126769195-T-G

Variant summary

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

The ENST00000520224.2(ENSG00000253573):​n.714+205A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,050 control chromosomes in the GnomAD database, including 10,825 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 0.28 (10825 hom., cov: 32)
• Consequence: ENSG00000253573 ENST00000520224.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186

Genes affected

ENSG00000253573 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375751	NR_188069.1	n.544+55521T>G		intron_variant
LOC105375751	NR_188070.1	n.545-24586T>G		intron_variant
LOC105375751	NR_188071.1	n.735-24586T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253573	ENST00000520224.2	n.714+205A>C		intron_variant		3
PCAT1	ENST00000645198.1	n.21+55521T>G		intron_variant
PCAT1	ENST00000645463.1	n.672+55521T>G		intron_variant
PCAT1	ENST00000647190.2	n.473+55389T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43125 AN: 151932 Hom.: 10767 Cov.: 32

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.0828

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0957

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0969

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.284 AC: 43250 AN: 152050 Hom.: 10825 Cov.: 32 AF XY: 0.282 AC XY: 20952 AN XY: 74322

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.0828

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0957

Gnomad4 NFE AF: 0.0969

Gnomad4 OTH AF: 0.257

Alfa AF: 0.122 Hom.: 3052

Bravo AF: 0.318

Asia WGS AF: 0.258 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12543473; hg19: chr8-127781440;