8-100800928-A-G

Variant names:

• chr8-100800928-A-G
• rs3847153

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 0.129 in 151,490 control chromosomes in the GnomAD database, including 1,897 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 0.13 (1897 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

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 (EAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19526 AN: 151372 Hom.: 1885 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0623

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.0810

Gnomad FIN AF: 0.0562

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0564

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.129 AC: 19587 AN: 151490 Hom.: 1897 Cov.: 31 AF XY: 0.132 AC XY: 9801 AN XY: 73988

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.0623

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.0814

Gnomad4 FIN AF: 0.0562

Gnomad4 NFE AF: 0.0564

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0710 Hom.: 1175

Bravo AF: 0.148

Asia WGS AF: 0.181 AC: 628 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	1.8
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3847153; hg19: chr8-101813156;