rs3760019

Variant names:

• chr16-55654385-C-T
• rs3760019
• XR_007065075.1:n.516-446G>A

Variant summary

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

The XR_007065075.1(LOC124903693):​n.516-446G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 152,052 control chromosomes in the GnomAD database, including 42,836 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 0.75 (42836 hom., cov: 31)
• Consequence: LOC124903693 XR_007065075.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.456
• Publications: 1 publications found

Genes affected

LOC124903693 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113742 AN: 151934 Hom.: 42799 Cov.: 31

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.749 AC: 113843 AN: 152052 Hom.: 42836 Cov.: 31 AF XY: 0.752 AC XY: 55893 AN XY: 74314

African (AFR) AF: 0.809 AC: 33568 AN: 41474

American (AMR) AF: 0.783 AC: 11979 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2451 AN: 3468

East Asian (EAS) AF: 0.708 AC: 3630 AN: 5124

South Asian (SAS) AF: 0.729 AC: 3507 AN: 4812

European-Finnish (FIN) AF: 0.736 AC: 7793 AN: 10586

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.715 AC: 48588 AN: 67980

Other (OTH) AF: 0.733 AC: 1546 AN: 2108

Alfa AF: 0.665 Hom.: 2157

Bravo AF: 0.756

Asia WGS AF: 0.715 AC: 2484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.49
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs3760019; hg19: chr16-55688297;