rs4548893

chr16-31353172-C-T

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 0.198 in 151,820 control chromosomes in the GnomAD database, including 3,163 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 0.20 (3163 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30029 AN: 151702 Hom.: 3161 Cov.: 30

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.00985

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.198 AC: 30051 AN: 151820 Hom.: 3163 Cov.: 30 AF XY: 0.197 AC XY: 14613 AN XY: 74228

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.00968

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.210

Alfa AF: 0.202 Hom.: 2956

Bravo AF: 0.197

Asia WGS AF: 0.130 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	7.6
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4548893; hg19: chr16-31364493;