chr16-55292892-A-G

Position:

• chr16-55292892-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558730.2(ENSG00000259283):​n.89-10228T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,598 control chromosomes in the GnomAD database, including 11,803 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 0.39 (11803 hom., cov: 30)
• Consequence: ENST00000558730.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000558730.2	n.89-10228T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.389 AC: 58910 AN: 151480 Hom.: 11790 Cov.: 30

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.389 AC: 58964 AN: 151598 Hom.: 11803 Cov.: 30 AF XY: 0.393 AC XY: 29074 AN XY: 74026

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.384

Alfa AF: 0.357 Hom.: 20010

Bravo AF: 0.392

Asia WGS AF: 0.563 AC: 1958 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	0.42
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11860394; hg19: chr16-55326804;