rs1363120

Variant names:

• chr19-18371494-C-G
• rs1363120

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 0.764 in 151,970 control chromosomes in the GnomAD database, including 44,873 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 0.76 (44873 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 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: 0.764 AC: 116030 AN: 151852 Hom.: 44856 Cov.: 29

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.764 AC: 116094 AN: 151970 Hom.: 44873 Cov.: 29 AF XY: 0.766 AC XY: 56904 AN XY: 74274

African (AFR) AF: 0.643 AC: 26619 AN: 41424

American (AMR) AF: 0.809 AC: 12334 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2940 AN: 3472

East Asian (EAS) AF: 0.824 AC: 4229 AN: 5132

South Asian (SAS) AF: 0.708 AC: 3412 AN: 4816

European-Finnish (FIN) AF: 0.880 AC: 9327 AN: 10596

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54656 AN: 67970

Other (OTH) AF: 0.759 AC: 1601 AN: 2108

Alfa AF: 0.790 Hom.: 5926

Bravo AF: 0.756

Asia WGS AF: 0.725 AC: 2526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.67
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1363120; hg19: chr19-18482304;