rs2048268

Variant names:

• chr4-57737417-A-G
• rs2048268

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 0.15 in 152,096 control chromosomes in the GnomAD database, including 4,627 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 0.15 (4627 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 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: 0.150 AC: 22771 AN: 151978 Hom.: 4595 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.00577

Gnomad EAS AF: 0.0885

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.00631

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00507

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.150 AC: 22875 AN: 152096 Hom.: 4627 Cov.: 32 AF XY: 0.150 AC XY: 11139 AN XY: 74380

African (AFR) AF: 0.458 AC: 18932 AN: 41372

American (AMR) AF: 0.146 AC: 2234 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00577 AC: 20 AN: 3468

East Asian (EAS) AF: 0.0895 AC: 463 AN: 5176

South Asian (SAS) AF: 0.112 AC: 540 AN: 4828

European-Finnish (FIN) AF: 0.00631 AC: 67 AN: 10626

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00507 AC: 345 AN: 68026

Other (OTH) AF: 0.125 AC: 264 AN: 2112

Alfa AF: 0.0521 Hom.: 2553

Bravo AF: 0.175

Asia WGS AF: 0.123 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.43
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs2048268; hg19: chr4-58603583;