chr8-102125817-A-G

Variant names:

• chr8-102125817-A-G
• rs648119

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;