16-58944346-G-T

Position:

• chr16-58944346-G-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 0.856 in 152,194 control chromosomes in the GnomAD database, including 56,033 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 0.86 (56033 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.58944346G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000245768	ENST00000500117.1	n.680-119836G>T		intron_variant		2
ENSG00000245768	ENST00000657379.1	n.651-119836G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130237 AN: 152076 Hom.: 55979 Cov.: 32

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.856 AC: 130352 AN: 152194 Hom.: 56033 Cov.: 32 AF XY: 0.864 AC XY: 64275 AN XY: 74412

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.855

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.930

Gnomad4 SAS AF: 0.894

Gnomad4 FIN AF: 0.933

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.812

Alfa AF: 0.822 Hom.: 23597

Bravo AF: 0.854

Asia WGS AF: 0.910 AC: 3163 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1865968; hg19: chr16-58978250;