3-80361009-T-G

Variant names:

• chr3-80361009-T-G
• rs2340388

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 0.138 in 151,928 control chromosomes in the GnomAD database, including 2,437 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 (2437 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 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: 0.138 AC: 20889 AN: 151810 Hom.: 2434 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.0644

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0629

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0527

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.138 AC: 20922 AN: 151928 Hom.: 2437 Cov.: 32 AF XY: 0.141 AC XY: 10467 AN XY: 74236

African (AFR) AF: 0.245 AC: 10180 AN: 41470

American (AMR) AF: 0.168 AC: 2552 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.0644 AC: 223 AN: 3462

East Asian (EAS) AF: 0.523 AC: 2687 AN: 5134

South Asian (SAS) AF: 0.154 AC: 744 AN: 4824

European-Finnish (FIN) AF: 0.0629 AC: 666 AN: 10596

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0527 AC: 3580 AN: 67912

Other (OTH) AF: 0.123 AC: 259 AN: 2112

Alfa AF: 0.0983 Hom.: 157

Bravo AF: 0.153

Asia WGS AF: 0.278 AC: 963 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.99
DANN	Benign	0.71
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2340388; hg19: chr3-80410159;