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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903693	XR_007065075.1	n.516-446G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;