rs1362756

chr16-51424379-C-G

Variant summary

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

The ENST00000643262.1(ENSG00000260850):n.400-67820G>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 0.698 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: ENST00000643262.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC102723323	XR_933558.3	n.376-19751G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000643262.1	n.400-67820G>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.947

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.722

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1362756; hg19: chr16-51458290;