chr8-102125817-A-G

Position:

• chr8-102125817-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 0.491 in 151,786 control chromosomes in the GnomAD database, including 18,687 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 0.49 (18687 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74517 AN: 151668 Hom.: 18676 Cov.: 30

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.491 AC: 74569 AN: 151786 Hom.: 18687 Cov.: 30 AF XY: 0.487 AC XY: 36143 AN XY: 74156

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.489

Alfa AF: 0.522 Hom.: 26400

Bravo AF: 0.481

Asia WGS AF: 0.461 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs648119; hg19: chr8-103138045;