19-44919689-A-G

Variant names:

• chr19-44919689-A-G
• rs4420638

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 0.18 in 151,786 control chromosomes in the GnomAD database, including 2,566 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: 𝑓 0.18 (2566 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: -1.31
• Publications: 541 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 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: 0.180 AC: 27280 AN: 151670 Hom.: 2557 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.180 AC: 27333 AN: 151786 Hom.: 2566 Cov.: 31 AF XY: 0.186 AC XY: 13792 AN XY: 74186

African (AFR) AF: 0.204 AC: 8438 AN: 41374

American (AMR) AF: 0.110 AC: 1682 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3468

East Asian (EAS) AF: 0.113 AC: 585 AN: 5160

South Asian (SAS) AF: 0.131 AC: 629 AN: 4812

European-Finnish (FIN) AF: 0.292 AC: 3070 AN: 10524

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.175 AC: 11884 AN: 67908

Other (OTH) AF: 0.143 AC: 301 AN: 2106

Alfa AF: 0.172 Hom.: 6776

Bravo AF: 0.168

Asia WGS AF: 0.180 AC: 627 AN: 3478

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

Department of Ophthalmology and Visual Sciences Kyoto University

Significance: not provided

Review Status: no classification provided

Collection Method: not provided

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.48
DANN	Benign	0.59
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4420638; hg19: chr19-45422946;