rs1560723

Variant names:

• chr19-50897100-A-G
• rs1560723

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 0.129 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.437 AC: 18070 AN: 41316

American (AMR) AF: 0.0543 AC: 829 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.00260 AC: 9 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5168

South Asian (SAS) AF: 0.0125 AC: 60 AN: 4810

European-Finnish (FIN) AF: 0.000755 AC: 8 AN: 10592

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.00482 AC: 328 AN: 67980

Other (OTH) AF: 0.110 AC: 232 AN: 2104

Alfa AF: 0.0496 Hom.: 1594

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1560723; hg19: chr19-51400356;