rs4488454

Variant names:

• chr16-87535529-C-G
• rs4488454

Your query was ambiguous. Multiple possible variants found:

• chr16-87535529-C-G
• chr16-87535529-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 0.53 in 151,946 control chromosomes in the GnomAD database, including 22,332 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 0.53 (22332 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.617 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: 0.530 AC: 80524 AN: 151828 Hom.: 22329 Cov.: 31

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.530 AC: 80534 AN: 151946 Hom.: 22332 Cov.: 31 AF XY: 0.520 AC XY: 38610 AN XY: 74258

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.556

Alfa AF: 0.423 Hom.: 1173

Bravo AF: 0.511

Asia WGS AF: 0.307 AC: 1069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
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: rs4488454; hg19: chr16-87569135;