19-5522345-T-C

Variant names:

• chr19-5522345-T-C
• rs385839

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 0.522 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.521 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

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.516

Alfa AF: 0.477 Hom.: 35656

Bravo AF: 0.533

Asia WGS AF: 0.588 AC: 2044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs385839; hg19: chr19-5522356;