rs2048554

Variant names:

• chr5-19348755-G-A
• rs2048554

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 0.405 in 151,718 control chromosomes in the GnomAD database, including 13,147 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 0.40 (13147 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.5 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: 0.405 AC: 61388 AN: 151600 Hom.: 13144 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.405 AC: 61415 AN: 151718 Hom.: 13147 Cov.: 32 AF XY: 0.401 AC XY: 29749 AN XY: 74112

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.401

Alfa AF: 0.452 Hom.: 8915

Bravo AF: 0.404

Asia WGS AF: 0.273 AC: 949 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.40
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2048554; hg19: chr5-19348864;