rs3108919

Variant names:

• chr8-100829318-T-C
• rs3108919

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 0.441 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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.828 AC: 34366 AN: 41480

American (AMR) AF: 0.409 AC: 6251 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1215 AN: 3466

East Asian (EAS) AF: 0.463 AC: 2391 AN: 5168

South Asian (SAS) AF: 0.283 AC: 1367 AN: 4826

European-Finnish (FIN) AF: 0.237 AC: 2501 AN: 10574

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17763 AN: 67970

Other (OTH) AF: 0.427 AC: 901 AN: 2112

Alfa AF: 0.339 Hom.: 33584

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
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs3108919; hg19: chr8-101841546;