rs3108919

Positions:

• chr8-100829318-T-C

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 0.441 in 152,098 control chromosomes in the GnomAD database, including 19,589 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 0.44 (19589 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 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: 0.441 AC: 67035 AN: 151980 Hom.: 19536 Cov.: 32

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.441 AC: 67150 AN: 152098 Hom.: 19589 Cov.: 32 AF XY: 0.439 AC XY: 32642 AN XY: 74382

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.427

Alfa AF: 0.301 Hom.: 15700

Bravo AF: 0.474

Asia WGS AF: 0.376 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.62
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3108919; hg19: chr8-101841546;