rs1469444

Variant names:

• chr5-25913556-G-A
• rs1469444

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 152,030 control chromosomes in the GnomAD database, including 44,862 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 (44862 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.813 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: 0.765 AC: 116136 AN: 151908 Hom.: 44845 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.764 AC: 116197 AN: 152030 Hom.: 44862 Cov.: 32 AF XY: 0.767 AC XY: 57002 AN XY: 74322

African (AFR) AF: 0.660 AC: 27341 AN: 41446

American (AMR) AF: 0.721 AC: 10994 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.827 AC: 2868 AN: 3470

East Asian (EAS) AF: 0.751 AC: 3877 AN: 5160

South Asian (SAS) AF: 0.824 AC: 3980 AN: 4832

European-Finnish (FIN) AF: 0.849 AC: 8990 AN: 10588

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55636 AN: 67972

Other (OTH) AF: 0.765 AC: 1614 AN: 2110

Alfa AF: 0.777 Hom.: 5957

Bravo AF: 0.746

Asia WGS AF: 0.804 AC: 2784 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.30
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1469444; hg19: chr5-25913665;