rs2206185

Variant names:

• chr6-104219784-C-G
• rs2206185

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 0.135 in 151,894 control chromosomes in the GnomAD database, including 1,550 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 0.13 (1550 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20425 AN: 151776 Hom.: 1540 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0260

Gnomad EAS AF: 0.0911

Gnomad SAS AF: 0.0957

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.135 AC: 20477 AN: 151894 Hom.: 1550 Cov.: 32 AF XY: 0.134 AC XY: 9936 AN XY: 74260

African (AFR) AF: 0.199 AC: 8219 AN: 41396

American (AMR) AF: 0.139 AC: 2125 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0260 AC: 90 AN: 3468

East Asian (EAS) AF: 0.0909 AC: 468 AN: 5148

South Asian (SAS) AF: 0.0958 AC: 461 AN: 4812

European-Finnish (FIN) AF: 0.136 AC: 1439 AN: 10564

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.107 AC: 7294 AN: 67944

Other (OTH) AF: 0.110 AC: 232 AN: 2110

Alfa AF: 0.132 Hom.: 167

Bravo AF: 0.139

Asia WGS AF: 0.140 AC: 483 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.72
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs2206185; hg19: chr6-104667659;