19-57227879-A-G

Variant names:

• chr19-57227879-A-G
• rs2361128

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 0.543 in 152,138 control chromosomes in the GnomAD database, including 23,597 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 0.54 (23597 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.416
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 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: 0.543 AC: 82561 AN: 152020 Hom.: 23590 Cov.: 33

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.543 AC: 82589 AN: 152138 Hom.: 23597 Cov.: 33 AF XY: 0.548 AC XY: 40774 AN XY: 74364

African (AFR) AF: 0.376 AC: 15611 AN: 41504

American (AMR) AF: 0.618 AC: 9454 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2145 AN: 3472

East Asian (EAS) AF: 0.846 AC: 4386 AN: 5186

South Asian (SAS) AF: 0.693 AC: 3344 AN: 4828

European-Finnish (FIN) AF: 0.646 AC: 6827 AN: 10560

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.576 AC: 39160 AN: 67984

Other (OTH) AF: 0.528 AC: 1111 AN: 2106

Alfa AF: 0.566 Hom.: 41515

Bravo AF: 0.535

Asia WGS AF: 0.715 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.8
DANN	Benign	0.79
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs2361128; hg19: chr19-57739247;