rs3760019

chr16-55654385-C-T

Variant summary

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

The XR_007065075.1(LOC124903693):n.516-446G>A 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 0.749 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.456

Genes affected

LOC124903693 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124903693	XR_007065075.1	n.516-446G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.733

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3760019; hg19: chr16-55688297;