chr16-51426960-A-G

Position:

• chr16-51426960-A-G

Variant summary

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

The ENST00000642667.1(ENSG00000285367):​n.393-10397A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 152,032 control chromosomes in the GnomAD database, including 19,348 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 0.48 (19348 hom., cov: 32)
• Consequence: ENSG00000285367 ENST00000642667.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92

Genes affected

ENSG00000285367 (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 (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723323	XR_933558.3	n.376-22332T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285367	ENST00000642667.1	n.393-10397A>G		intron_variant
ENSG00000260850	ENST00000643262.1	n.399+68142T>C		intron_variant
ENSG00000260850	ENST00000646267.1	n.390-22332T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73579 AN: 151914 Hom.: 19312 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.484 AC: 73654 AN: 152032 Hom.: 19348 Cov.: 32 AF XY: 0.493 AC XY: 36607 AN XY: 74300

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.496

Alfa AF: 0.492 Hom.: 23546

Bravo AF: 0.483

Asia WGS AF: 0.769 AC: 2673 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.041
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2063099; hg19: chr16-51460871;