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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723323	XR_933558.3	n.376-19751G>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285367	ENST00000642667.1	n.392+12326C>G		intron_variant	Intron 2 of 3
ENSG00000260850	ENST00000643262.1	n.400-67820G>C		intron_variant	Intron 2 of 2
ENSG00000260850	ENST00000646267.1	n.390-19751G>C		intron_variant	Intron 2 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs1362756; hg19: chr16-51458290;