rs4129374

Variant names:

• chr6-3204445-C-A
• rs4129374

Your query was ambiguous. Multiple possible variants found:

• chr6-3204445-C-A
• chr6-3204445-C-G

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 0.687 in 151,850 control chromosomes in the GnomAD database, including 36,171 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 0.69 (36171 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.719 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: 0.687 AC: 104237 AN: 151732 Hom.: 36140 Cov.: 30

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.687 AC: 104314 AN: 151850 Hom.: 36171 Cov.: 30 AF XY: 0.682 AC XY: 50588 AN XY: 74178

African (AFR) AF: 0.690 AC: 28545 AN: 41374

American (AMR) AF: 0.698 AC: 10652 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2330 AN: 3464

East Asian (EAS) AF: 0.492 AC: 2541 AN: 5164

South Asian (SAS) AF: 0.487 AC: 2343 AN: 4814

European-Finnish (FIN) AF: 0.613 AC: 6424 AN: 10486

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.724 AC: 49211 AN: 67970

Other (OTH) AF: 0.681 AC: 1437 AN: 2110

Alfa AF: 0.702 Hom.: 49390

Bravo AF: 0.692

Asia WGS AF: 0.510 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.45
DANN	Benign	0.15
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs4129374; hg19: chr6-3204679;