chr8-29486945-A-G

Variant names:

• chr8-29486945-A-G
• rs12548021

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.553
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.205 AC: 8490 AN: 41504

American (AMR) AF: 0.387 AC: 5912 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1161 AN: 3472

East Asian (EAS) AF: 0.193 AC: 999 AN: 5174

South Asian (SAS) AF: 0.246 AC: 1187 AN: 4818

European-Finnish (FIN) AF: 0.423 AC: 4472 AN: 10566

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26316 AN: 67976

Other (OTH) AF: 0.309 AC: 652 AN: 2112

Alfa AF: 0.360 Hom.: 31673

Bravo AF: 0.321

Asia WGS AF: 0.217 AC: 756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.4
DANN	Benign	0.69
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs12548021; hg19: chr8-29344462;