8-48899642-A-T

Variant names:

• chr8-48899642-A-T
• rs12155623

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 0.655 in 152,068 control chromosomes in the GnomAD database, including 34,153 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 0.65 (34153 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.73
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 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: 0.654 AC: 99444 AN: 151950 Hom.: 34092 Cov.: 32

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.692

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.655 AC: 99564 AN: 152068 Hom.: 34153 Cov.: 32 AF XY: 0.651 AC XY: 48409 AN XY: 74308

African (AFR) AF: 0.879 AC: 36490 AN: 41530

American (AMR) AF: 0.631 AC: 9633 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2159 AN: 3466

East Asian (EAS) AF: 0.341 AC: 1759 AN: 5162

South Asian (SAS) AF: 0.714 AC: 3431 AN: 4808

European-Finnish (FIN) AF: 0.511 AC: 5390 AN: 10554

Middle Eastern (MID) AF: 0.697 AC: 202 AN: 290

European-Non Finnish (NFE) AF: 0.569 AC: 38668 AN: 67970

Other (OTH) AF: 0.640 AC: 1351 AN: 2112

Alfa AF: 0.577 Hom.: 14186

Bravo AF: 0.665

Asia WGS AF: 0.564 AC: 1963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.3
DANN	Benign	0.18
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs12155623; hg19: chr8-49812201;