16-30634323-A-T

Position:

• chr16-30634323-A-T

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 0.462 in 151,974 control chromosomes in the GnomAD database, including 18,813 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 0.46 (18813 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.30634323A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70154 AN: 151856 Hom.: 18791 Cov.: 32

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.462 AC: 70212 AN: 151974 Hom.: 18813 Cov.: 32 AF XY: 0.460 AC XY: 34195 AN XY: 74262

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.418

Alfa AF: 0.278 Hom.: 735

Bravo AF: 0.473

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	3.6
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7194347; hg19: chr16-30645644;