chr19-44839558-G-C

Variant names:

• chr19-44839558-G-C
• rs1466435

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 0.068 in 152,098 control chromosomes in the GnomAD database, including 475 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 0.068 (475 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 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: 0.0679 AC: 10315 AN: 151980 Hom.: 470 Cov.: 30

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.0438

Gnomad ASJ AF: 0.0844

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0247

Gnomad FIN AF: 0.0226

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0481

Gnomad OTH AF: 0.0646

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

GnomAD4 genome AF: 0.0680 AC: 10347 AN: 152098 Hom.: 475 Cov.: 30 AF XY: 0.0647 AC XY: 4812 AN XY: 74374

African (AFR) AF: 0.134 AC: 5549 AN: 41478

American (AMR) AF: 0.0437 AC: 667 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0844 AC: 293 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5176

South Asian (SAS) AF: 0.0251 AC: 121 AN: 4816

European-Finnish (FIN) AF: 0.0226 AC: 240 AN: 10600

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0481 AC: 3268 AN: 67994

Other (OTH) AF: 0.0639 AC: 135 AN: 2112

Alfa AF: 0.0530 Hom.: 120

Bravo AF: 0.0717

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.67
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1466435; hg19: chr19-45342815;