rs1362756

Variant names:

• chr16-51424379-C-G
• rs1362756
• ENST00000642667.1:n.392+12326C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642667.1(ENSG00000285367):​n.392+12326C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 151,952 control chromosomes in the GnomAD database, including 37,671 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 0.70 (37671 hom., cov: 31)
• Consequence: ENSG00000285367 ENST00000642667.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327
• Publications: 22 publications found

Genes affected

ENSG00000285367 (HGNC:58539):

ENSG00000260850 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642667.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285367	ENST00000642667.1		n.392+12326C>G		intron	N/A
	ENSG00000260850	ENST00000643262.1		n.400-67820G>C		intron	N/A
	ENSG00000260850	ENST00000646267.1		n.390-19751G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105984 AN: 151834 Hom.: 37628 Cov.: 31

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.698 AC: 106084 AN: 151952 Hom.: 37671 Cov.: 31 AF XY: 0.704 AC XY: 52290 AN XY: 74270

African (AFR) AF: 0.589 AC: 24377 AN: 41402

American (AMR) AF: 0.783 AC: 11958 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2698 AN: 3470

East Asian (EAS) AF: 0.947 AC: 4893 AN: 5168

South Asian (SAS) AF: 0.794 AC: 3814 AN: 4802

European-Finnish (FIN) AF: 0.715 AC: 7551 AN: 10562

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48385 AN: 67964

Other (OTH) AF: 0.722 AC: 1526 AN: 2114

Alfa AF: 0.722 Hom.: 22144

Bravo AF: 0.700

Asia WGS AF: 0.838 AC: 2915 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.72
PhyloP100		0.33

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1362756;

hg19: chr16-51458290;