chr16-12620537-A-C

Position:

• chr16-12620537-A-C

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 0.549 in 151,972 control chromosomes in the GnomAD database, including 23,486 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 0.55 (23486 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536

Genes affected

(HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.12620537A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83463 AN: 151854 Hom.: 23480 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.549 AC: 83492 AN: 151972 Hom.: 23486 Cov.: 32 AF XY: 0.551 AC XY: 40948 AN XY: 74268

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.560

Alfa AF: 0.581 Hom.: 35688

Bravo AF: 0.551

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.94
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4780469; hg19: chr16-12714394;