3-185911780-A-G

Variant names:

• chr3-185911780-A-G
• rs2002675

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 0.353 in 151,886 control chromosomes in the GnomAD database, including 9,851 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 0.35 (9851 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 28 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 = 0.417 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53534 AN: 151768 Hom.: 9838 Cov.: 31

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.353 AC: 53569 AN: 151886 Hom.: 9851 Cov.: 31 AF XY: 0.346 AC XY: 25687 AN XY: 74216

African (AFR) AF: 0.299 AC: 12409 AN: 41436

American (AMR) AF: 0.263 AC: 4017 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1142 AN: 3466

East Asian (EAS) AF: 0.153 AC: 790 AN: 5164

South Asian (SAS) AF: 0.271 AC: 1301 AN: 4804

European-Finnish (FIN) AF: 0.384 AC: 4053 AN: 10554

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.421 AC: 28567 AN: 67892

Other (OTH) AF: 0.336 AC: 706 AN: 2104

Alfa AF: 0.398 Hom.: 36640

Bravo AF: 0.344

Asia WGS AF: 0.230 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.12
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs2002675; hg19: chr3-185629568;