19-29580124-C-G

Variant names:

• chr19-29580124-C-G
• rs11670734

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 0.63 in 152,100 control chromosomes in the GnomAD database, including 30,688 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 0.63 (30688 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.714 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: 0.630 AC: 95812 AN: 151980 Hom.: 30672 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.630 AC: 95859 AN: 152100 Hom.: 30688 Cov.: 32 AF XY: 0.636 AC XY: 47260 AN XY: 74356

African (AFR) AF: 0.523 AC: 21692 AN: 41476

American (AMR) AF: 0.726 AC: 11096 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2609 AN: 3468

East Asian (EAS) AF: 0.713 AC: 3678 AN: 5158

South Asian (SAS) AF: 0.694 AC: 3347 AN: 4824

European-Finnish (FIN) AF: 0.711 AC: 7521 AN: 10584

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43605 AN: 67980

Other (OTH) AF: 0.670 AC: 1413 AN: 2110

Alfa AF: 0.627 Hom.: 3605

Bravo AF: 0.629

Asia WGS AF: 0.688 AC: 2393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.1
DANN	Benign	0.48
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs11670734; hg19: chr19-30071031;