chr3-102091875-A-G

Variant names:

• chr3-102091875-A-G
• rs9813042

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 0.298 in 152,096 control chromosomes in the GnomAD database, including 7,402 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 0.30 (7402 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 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: 0.298 AC: 45289 AN: 151978 Hom.: 7398 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.298 AC: 45318 AN: 152096 Hom.: 7402 Cov.: 32 AF XY: 0.299 AC XY: 22247 AN XY: 74340

African (AFR) AF: 0.173 AC: 7189 AN: 41518

American (AMR) AF: 0.332 AC: 5067 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 986 AN: 3470

East Asian (EAS) AF: 0.162 AC: 837 AN: 5172

South Asian (SAS) AF: 0.213 AC: 1027 AN: 4822

European-Finnish (FIN) AF: 0.401 AC: 4226 AN: 10544

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24858 AN: 67982

Other (OTH) AF: 0.295 AC: 621 AN: 2108

Alfa AF: 0.304 Hom.: 5499

Bravo AF: 0.287

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.6
DANN	Benign	0.72
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs9813042; hg19: chr3-101810719;