rs520916

Variant names:

• chr1-12164396-A-G
• rs520916

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 0.161 in 151,920 control chromosomes in the GnomAD database, including 4,670 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 0.16 (4670 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 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: 0.161 AC: 24456 AN: 151802 Hom.: 4654 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0745

Gnomad ASJ AF: 0.0445

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.0257

Gnomad FIN AF: 0.0168

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0462

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.161 AC: 24534 AN: 151920 Hom.: 4670 Cov.: 32 AF XY: 0.155 AC XY: 11472 AN XY: 74252

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.0743

Gnomad4 ASJ AF: 0.0445

Gnomad4 EAS AF: 0.0147

Gnomad4 SAS AF: 0.0253

Gnomad4 FIN AF: 0.0168

Gnomad4 NFE AF: 0.0462

Gnomad4 OTH AF: 0.140

Alfa AF: 0.153 Hom.: 635

Bravo AF: 0.179

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.015
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs520916; hg19: chr1-12224453; COSMIC: COSV66163600;