rs4500724

Positions:

• chr16-55649465-G-A

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 0.3 in 151,994 control chromosomes in the GnomAD database, including 7,074 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 0.30 (7074 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 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: 0.299 AC: 45475 AN: 151876 Hom.: 7060 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.300 AC: 45530 AN: 151994 Hom.: 7074 Cov.: 32 AF XY: 0.297 AC XY: 22083 AN XY: 74286

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.270

Alfa AF: 0.291 Hom.: 3201

Bravo AF: 0.298

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.43
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4500724; hg19: chr16-55683377;