rs6599400

Variant names:

• chr4-1783298-A-C
• rs6599400

Your query was ambiguous. Multiple possible variants found:

• chr4-1783298-A-C
• chr4-1783298-A-G
• chr4-1783298-A-T

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 0.649 in 151,036 control chromosomes in the GnomAD database, including 32,679 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 0.65 (32679 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 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: 0.650 AC: 98022 AN: 150918 Hom.: 32658 Cov.: 26

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.649 AC: 98084 AN: 151036 Hom.: 32679 Cov.: 26 AF XY: 0.662 AC XY: 48781 AN XY: 73742

African (AFR) AF: 0.523 AC: 21489 AN: 41078

American (AMR) AF: 0.712 AC: 10805 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1988 AN: 3452

East Asian (EAS) AF: 0.906 AC: 4643 AN: 5124

South Asian (SAS) AF: 0.781 AC: 3712 AN: 4750

European-Finnish (FIN) AF: 0.839 AC: 8781 AN: 10460

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44629 AN: 67722

Other (OTH) AF: 0.640 AC: 1339 AN: 2092

Alfa AF: 0.642 Hom.: 57722

Bravo AF: 0.631

Asia WGS AF: 0.821 AC: 2854 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.80
DANN	Benign	0.53
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6599400; hg19: chr4-1785025;