rs5016499

Variant names:

• chr4-182919745-G-T
• rs5016499

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 0.333 in 151,642 control chromosomes in the GnomAD database, including 8,834 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 0.33 (8834 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 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: 0.333 AC: 50441 AN: 151524 Hom.: 8821 Cov.: 30

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.333 AC: 50488 AN: 151642 Hom.: 8834 Cov.: 30 AF XY: 0.335 AC XY: 24811 AN XY: 74088

African (AFR) AF: 0.452 AC: 18662 AN: 41268

American (AMR) AF: 0.243 AC: 3698 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3468

East Asian (EAS) AF: 0.367 AC: 1883 AN: 5136

South Asian (SAS) AF: 0.294 AC: 1402 AN: 4772

European-Finnish (FIN) AF: 0.364 AC: 3837 AN: 10534

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19307 AN: 67898

Other (OTH) AF: 0.295 AC: 624 AN: 2112

Alfa AF: 0.297 Hom.: 18870

Bravo AF: 0.329

Asia WGS AF: 0.361 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.2
DANN	Benign	0.84
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs5016499; hg19: chr4-183840898;