rs3924616

Variant names:

• chr5-23356864-A-G
• rs3924616

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 0.267 in 152,068 control chromosomes in the GnomAD database, including 5,676 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 0.27 (5676 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.491

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.444 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: 0.267 AC: 40578 AN: 151948 Hom.: 5667 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.267 AC: 40622 AN: 152068 Hom.: 5676 Cov.: 33 AF XY: 0.267 AC XY: 19825 AN XY: 74336

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.273

Alfa AF: 0.252 Hom.: 6698

Bravo AF: 0.271

Asia WGS AF: 0.323 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3924616; hg19: chr5-23356973;