rs4500724

Variant names:

• chr16-55649465-G-A
• rs4500724

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 0.3 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.369 AC: 15296 AN: 41424

American (AMR) AF: 0.250 AC: 3816 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 832 AN: 3470

East Asian (EAS) AF: 0.148 AC: 765 AN: 5184

South Asian (SAS) AF: 0.207 AC: 994 AN: 4810

European-Finnish (FIN) AF: 0.303 AC: 3189 AN: 10532

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.290 AC: 19730 AN: 67970

Other (OTH) AF: 0.270 AC: 571 AN: 2114

Alfa AF: 0.292 Hom.: 3605

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
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs4500724; hg19: chr16-55683377;