rs1448044

Variant names:

• chr5-44296884-G-A
• rs1448044

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 0.43 in 152,050 control chromosomes in the GnomAD database, including 15,239 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 0.43 (15239 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 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: 0.430 AC: 65255 AN: 151932 Hom.: 15212 Cov.: 33

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.430 AC: 65320 AN: 152050 Hom.: 15239 Cov.: 33 AF XY: 0.429 AC XY: 31848 AN XY: 74316

African (AFR) AF: 0.606 AC: 25132 AN: 41462

American (AMR) AF: 0.505 AC: 7711 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1074 AN: 3466

East Asian (EAS) AF: 0.511 AC: 2641 AN: 5172

South Asian (SAS) AF: 0.398 AC: 1919 AN: 4820

European-Finnish (FIN) AF: 0.326 AC: 3449 AN: 10582

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22126 AN: 67972

Other (OTH) AF: 0.415 AC: 875 AN: 2110

Alfa AF: 0.363 Hom.: 18288

Bravo AF: 0.453

Asia WGS AF: 0.512 AC: 1781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.51
DANN	Benign	0.30
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs1448044; hg19: chr5-44296986;