rs3212236

Variant names:

• chr6-24648227-T-C
• rs3212236

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 0.225 in 152,162 control chromosomes in the GnomAD database, including 4,842 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 0.23 (4842 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 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: 0.225 AC: 34233 AN: 152044 Hom.: 4841 Cov.: 31

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.225 AC: 34252 AN: 152162 Hom.: 4842 Cov.: 31 AF XY: 0.230 AC XY: 17134 AN XY: 74410

African (AFR) AF: 0.205 AC: 8490 AN: 41512

American (AMR) AF: 0.367 AC: 5616 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 728 AN: 3470

East Asian (EAS) AF: 0.632 AC: 3256 AN: 5154

South Asian (SAS) AF: 0.429 AC: 2069 AN: 4824

European-Finnish (FIN) AF: 0.124 AC: 1317 AN: 10610

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11838 AN: 67986

Other (OTH) AF: 0.243 AC: 514 AN: 2114

Alfa AF: 0.190 Hom.: 1258

Bravo AF: 0.240

Asia WGS AF: 0.504 AC: 1751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.84
DANN	Benign	0.74
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs3212236; hg19: chr6-24648455;