16-30129937-A-C

Position:

• chr16-30129937-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 0.417 in 151,046 control chromosomes in the GnomAD database, including 14,022 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 0.42 (14022 hom., cov: 29)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.30129937A>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.416 AC: 62838 AN: 150920 Hom.: 13992 Cov.: 29

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.417 AC: 62930 AN: 151046 Hom.: 14022 Cov.: 29 AF XY: 0.414 AC XY: 30504 AN XY: 73756

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.398

Alfa AF: 0.358 Hom.: 8132

Bravo AF: 0.429

Asia WGS AF: 0.435 AC: 1510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.4
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2005219; hg19: chr16-30141258;