19-5522345-T-C

Variant names:

• chr19-5522345-T-C
• rs385839

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 0.522 in 151,950 control chromosomes in the GnomAD database, including 21,044 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 0.52 (21044 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.517
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79145 AN: 151832 Hom.: 20999 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.522 AC: 79248 AN: 151950 Hom.: 21044 Cov.: 32 AF XY: 0.526 AC XY: 39103 AN XY: 74284

African (AFR) AF: 0.596 AC: 24676 AN: 41432

American (AMR) AF: 0.613 AC: 9358 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1747 AN: 3470

East Asian (EAS) AF: 0.567 AC: 2920 AN: 5148

South Asian (SAS) AF: 0.621 AC: 2993 AN: 4820

European-Finnish (FIN) AF: 0.461 AC: 4874 AN: 10574

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.455 AC: 30920 AN: 67934

Other (OTH) AF: 0.516 AC: 1086 AN: 2106

Alfa AF: 0.484 Hom.: 79076

Bravo AF: 0.533

Asia WGS AF: 0.588 AC: 2044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	8.4
DANN	Benign	0.46
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs385839; hg19: chr19-5522356;