rs1558448

Variant names:

• chr4-16358948-T-C
• rs1558448

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 0.24 in 152,132 control chromosomes in the GnomAD database, including 6,058 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 0.24 (6058 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 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: 0.240 AC: 36463 AN: 152014 Hom.: 6049 Cov.: 33

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0512

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.240 AC: 36504 AN: 152132 Hom.: 6058 Cov.: 33 AF XY: 0.234 AC XY: 17377 AN XY: 74394

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.0514

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.213

Alfa AF: 0.213 Hom.: 550

Bravo AF: 0.251

Asia WGS AF: 0.105 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	1.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1558448; hg19: chr4-16360571;