rs4420638

Variant names:

• chr19-44919689-A-G
• rs4420638

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.143

Alfa AF: 0.169 Hom.: 1920

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

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Department of Ophthalmology and Visual Sciences Kyoto University

Significance: not provided

Review Status: no classification provided

Collection Method: not provided

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Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4420638; hg19: chr19-45422946;