8-5390815-G-C

Variant names:

• chr8-5390815-G-C
• rs10866988

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 0.506 in 152,002 control chromosomes in the GnomAD database, including 19,407 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 0.51 (19407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.538 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: 0.505 AC: 76761 AN: 151882 Hom.: 19374 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.506 AC: 76850 AN: 152002 Hom.: 19407 Cov.: 32 AF XY: 0.510 AC XY: 37872 AN XY: 74284

African (AFR) AF: 0.517 AC: 21441 AN: 41444

American (AMR) AF: 0.503 AC: 7681 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1728 AN: 3464

East Asian (EAS) AF: 0.504 AC: 2604 AN: 5166

South Asian (SAS) AF: 0.556 AC: 2681 AN: 4822

European-Finnish (FIN) AF: 0.503 AC: 5309 AN: 10546

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33692 AN: 67982

Other (OTH) AF: 0.509 AC: 1072 AN: 2106

Alfa AF: 0.366 Hom.: 938

Bravo AF: 0.503

Asia WGS AF: 0.540 AC: 1876 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	0.27
DANN	Benign	0.34
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs10866988; hg19: chr8-5248337;