8-29486945-A-G

Position:

• chr8-29486945-A-G

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 0.327 in 152,100 control chromosomes in the GnomAD database, including 8,708 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 0.33 (8708 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.553

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.29486945A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49651 AN: 151982 Hom.: 8703 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.327 AC: 49685 AN: 152100 Hom.: 8708 Cov.: 32 AF XY: 0.327 AC XY: 24314 AN XY: 74326

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.309

Alfa AF: 0.370 Hom.: 21118

Bravo AF: 0.321

Asia WGS AF: 0.217 AC: 756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12548021; hg19: chr8-29344462;