rs4839516

chr1-116197828-C-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 0.203 in 152,140 control chromosomes in the GnomAD database, including 4,065 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 (4065 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 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: 0.204 AC: 30947 AN: 152022 Hom.: 4062 Cov.: 32

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0192

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.203 AC: 30949 AN: 152140 Hom.: 4065 Cov.: 32 AF XY: 0.198 AC XY: 14724 AN XY: 74374

Gnomad4 AFR AF: 0.0620

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.0193

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.256

Alfa AF: 0.230 Hom.: 930

Bravo AF: 0.199

Asia WGS AF: 0.129 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.55
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: rs4839516; hg19: chr1-116740450;