rs16966229

Variant names:

• chr19-31741404-T-C
• rs16966229

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 0.0384 in 152,322 control chromosomes in the GnomAD database, including 296 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 0.038 (296 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 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: 0.0383 AC: 5829 AN: 152204 Hom.: 295 Cov.: 33

Gnomad AFR AF: 0.0458

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0878

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.0795

Gnomad FIN AF: 0.0298

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00823

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0384 AC: 5848 AN: 152322 Hom.: 296 Cov.: 33 AF XY: 0.0425 AC XY: 3169 AN XY: 74480

African (AFR) AF: 0.0457 AC: 1901 AN: 41584

American (AMR) AF: 0.0886 AC: 1356 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0109 AC: 38 AN: 3472

East Asian (EAS) AF: 0.235 AC: 1212 AN: 5164

South Asian (SAS) AF: 0.0785 AC: 379 AN: 4826

European-Finnish (FIN) AF: 0.0298 AC: 317 AN: 10626

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00823 AC: 560 AN: 68024

Other (OTH) AF: 0.0384 AC: 81 AN: 2112

Alfa AF: 0.0326 Hom.: 25

Bravo AF: 0.0429

Asia WGS AF: 0.142 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	8.5
DANN	Benign	0.42
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs16966229; hg19: chr19-32232310;