rs920417

Variant names:

• chr3-165173430-G-A
• rs920417

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 0.456 in 151,902 control chromosomes in the GnomAD database, including 17,280 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 0.46 (17280 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.565 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: 0.457 AC: 69299 AN: 151780 Hom.: 17280 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.456 AC: 69306 AN: 151902 Hom.: 17280 Cov.: 32 AF XY: 0.452 AC XY: 33536 AN XY: 74248

African (AFR) AF: 0.288 AC: 11949 AN: 41458

American (AMR) AF: 0.436 AC: 6647 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1757 AN: 3464

East Asian (EAS) AF: 0.191 AC: 987 AN: 5160

South Asian (SAS) AF: 0.376 AC: 1812 AN: 4818

European-Finnish (FIN) AF: 0.553 AC: 5832 AN: 10546

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38717 AN: 67894

Other (OTH) AF: 0.481 AC: 1014 AN: 2110

Alfa AF: 0.512 Hom.: 54948

Bravo AF: 0.436

Asia WGS AF: 0.245 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.1
DANN	Benign	0.69
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs920417; hg19: chr3-164891218;