rs2048554

Variant names:

• chr5-19348755-G-A
• rs2048554

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 0.405 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.299 AC: 12374 AN: 41430

American (AMR) AF: 0.509 AC: 7737 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1538 AN: 3468

East Asian (EAS) AF: 0.101 AC: 520 AN: 5160

South Asian (SAS) AF: 0.363 AC: 1746 AN: 4806

European-Finnish (FIN) AF: 0.411 AC: 4318 AN: 10516

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31744 AN: 67830

Other (OTH) AF: 0.401 AC: 846 AN: 2112

Alfa AF: 0.451 Hom.: 9760

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
PhyloP100		-0.086

Splicing

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

Other links and lift over

dbSNP: rs2048554; hg19: chr5-19348864;