rs1560723

Positions:

• chr19-50897100-A-G

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 0.129 in 151,918 control chromosomes in the GnomAD database, including 4,044 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 0.13 (4044 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19481 AN: 151800 Hom.: 4016 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0544

Gnomad ASJ AF: 0.00260

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0123

Gnomad FIN AF: 0.000755

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00484

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.129 AC: 19561 AN: 151918 Hom.: 4044 Cov.: 31 AF XY: 0.125 AC XY: 9249 AN XY: 74242

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.0543

Gnomad4 ASJ AF: 0.00260

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0125

Gnomad4 FIN AF: 0.000755

Gnomad4 NFE AF: 0.00482

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0316 Hom.: 732

Bravo AF: 0.147

Asia WGS AF: 0.0620 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.7
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1560723; hg19: chr19-51400356;