rs12611334

Variant names:

• chr19-39738769-C-G
• rs12611334

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 0.279 in 152,156 control chromosomes in the GnomAD database, including 6,343 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 0.28 (6343 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42459 AN: 152038 Hom.: 6341 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.279 AC: 42465 AN: 152156 Hom.: 6343 Cov.: 32 AF XY: 0.277 AC XY: 20613 AN XY: 74384

African (AFR) AF: 0.211 AC: 8759 AN: 41502

American (AMR) AF: 0.191 AC: 2913 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 909 AN: 3470

East Asian (EAS) AF: 0.168 AC: 869 AN: 5182

South Asian (SAS) AF: 0.296 AC: 1429 AN: 4820

European-Finnish (FIN) AF: 0.307 AC: 3246 AN: 10590

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23534 AN: 67994

Other (OTH) AF: 0.241 AC: 509 AN: 2114

Alfa AF: 0.325 Hom.: 1073

Bravo AF: 0.261

Asia WGS AF: 0.226 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.43
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs12611334; hg19: chr19-40229409;