rs3800406

Variant names:

• chr6-35165297-A-G
• rs3800406

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 0.0764 in 152,230 control chromosomes in the GnomAD database, including 601 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 0.076 (601 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 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: 0.0765 AC: 11634 AN: 152112 Hom.: 601 Cov.: 32

Gnomad AFR AF: 0.0202

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.0386

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0660

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

GnomAD4 genome AF: 0.0764 AC: 11626 AN: 152230 Hom.: 601 Cov.: 32 AF XY: 0.0783 AC XY: 5827 AN XY: 74416

African (AFR) AF: 0.0202 AC: 838 AN: 41560

American (AMR) AF: 0.0545 AC: 833 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0536 AC: 186 AN: 3470

East Asian (EAS) AF: 0.0153 AC: 79 AN: 5174

South Asian (SAS) AF: 0.0380 AC: 183 AN: 4818

European-Finnish (FIN) AF: 0.163 AC: 1722 AN: 10592

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7486 AN: 68012

Other (OTH) AF: 0.0653 AC: 138 AN: 2114

Alfa AF: 0.0943 Hom.: 200

Bravo AF: 0.0650

Asia WGS AF: 0.0230 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.49
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs3800406; hg19: chr6-35133074;