chr3-16568941-C-G

Variant names:

• chr3-16568941-C-G
• rs4685345

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 0.139 in 152,192 control chromosomes in the GnomAD database, including 1,878 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 0.14 (1878 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.413 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: 0.139 AC: 21210 AN: 152074 Hom.: 1874 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.0903

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.139 AC: 21228 AN: 152192 Hom.: 1878 Cov.: 33 AF XY: 0.143 AC XY: 10650 AN XY: 74408

African (AFR) AF: 0.118 AC: 4891 AN: 41530

American (AMR) AF: 0.211 AC: 3226 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0903 AC: 313 AN: 3468

East Asian (EAS) AF: 0.428 AC: 2209 AN: 5164

South Asian (SAS) AF: 0.196 AC: 945 AN: 4824

European-Finnish (FIN) AF: 0.126 AC: 1334 AN: 10588

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7958 AN: 67990

Other (OTH) AF: 0.128 AC: 270 AN: 2114

Alfa AF: 0.121 Hom.: 159

Bravo AF: 0.149

Asia WGS AF: 0.269 AC: 934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.92
DANN	Benign	0.55
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs4685345; hg19: chr3-16610448;