rs2206185

Positions:

• chr6-104219784-C-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0260

Gnomad4 EAS AF: 0.0909

Gnomad4 SAS AF: 0.0958

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.110

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2206185; hg19: chr6-104667659;