rs1457463

Positions:

• chr8-134087535-G-A
• chr8-134087535-G-T

Variant summary

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

The variant allele was found at a frequency of 0.597 in 152,184 control chromosomes in the GnomAD database, including 29,353 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 (29353 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.134087535G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90756 AN: 152066 Hom.: 29315 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.597 AC: 90849 AN: 152184 Hom.: 29353 Cov.: 32 AF XY: 0.584 AC XY: 43464 AN XY: 74390

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.586

Alfa AF: 0.554 Hom.: 22145

Bravo AF: 0.614

Asia WGS AF: 0.329 AC: 1147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.078
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1457463; hg19: chr8-135099778;