3-68699987-T-G

Variant names:

• chr3-68699987-T-G
• rs1504294

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.61 in 151,980 control chromosomes in the GnomAD database, including 29,351 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 0.61 (29351 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.65
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92649 AN: 151860 Hom.: 29361 Cov.: 31

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.619

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.610 AC: 92668 AN: 151980 Hom.: 29351 Cov.: 31 AF XY: 0.617 AC XY: 45807 AN XY: 74284

African (AFR) AF: 0.468 AC: 19397 AN: 41438

American (AMR) AF: 0.580 AC: 8848 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2205 AN: 3468

East Asian (EAS) AF: 0.931 AC: 4794 AN: 5150

South Asian (SAS) AF: 0.834 AC: 4021 AN: 4822

European-Finnish (FIN) AF: 0.738 AC: 7800 AN: 10570

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.643 AC: 43708 AN: 67946

Other (OTH) AF: 0.609 AC: 1287 AN: 2114

Alfa AF: 0.642 Hom.: 18687

Bravo AF: 0.590

Asia WGS AF: 0.792 AC: 2754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	20
DANN	Benign	0.69
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs1504294; hg19: chr3-68749138;