6-84853351-A-G

Variant names:

• chr6-84853351-A-G
• rs2224211

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 0.214 in 152,172 control chromosomes in the GnomAD database, including 3,851 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 0.21 (3851 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.277 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: 0.214 AC: 32590 AN: 152054 Hom.: 3849 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.214 AC: 32609 AN: 152172 Hom.: 3851 Cov.: 32 AF XY: 0.218 AC XY: 16240 AN XY: 74404

African (AFR) AF: 0.126 AC: 5228 AN: 41534

American (AMR) AF: 0.284 AC: 4338 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3470

East Asian (EAS) AF: 0.226 AC: 1167 AN: 5174

South Asian (SAS) AF: 0.221 AC: 1065 AN: 4812

European-Finnish (FIN) AF: 0.278 AC: 2944 AN: 10582

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16675 AN: 67994

Other (OTH) AF: 0.203 AC: 430 AN: 2114

Alfa AF: 0.233 Hom.: 10474

Bravo AF: 0.211

Asia WGS AF: 0.215 AC: 753 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	4.4
DANN	Benign	0.73
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2224211; hg19: chr6-85563069;