rs1448044

Variant names:

• chr5-44296884-G-A
• rs1448044

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 0.43 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.415

Alfa AF: 0.348 Hom.: 11629

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1448044; hg19: chr5-44296986;