rs45458507

Positions:

• chr3-117497574-A-G
• chr3-117497574-A-T

Variant summary

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

The XR_924361.3(LOC105374056):​n.14254A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0561 in 152,308 control chromosomes in the GnomAD database, including 279 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 0.056 (279 hom., cov: 32)
• Consequence: LOC105374056 XR_924361.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

LOC105374056 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374056	XR_924361.3	n.14254A>G		non_coding_transcript_exon_variant	1/4
LOC105374056	XR_007096021.1	n.14254A>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0561 AC: 8531 AN: 152188 Hom.: 278 Cov.: 32

Gnomad AFR AF: 0.0286

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0569

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0803

Gnomad FIN AF: 0.0573

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.0764

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

GnomAD4 genome AF: 0.0561 AC: 8541 AN: 152308 Hom.: 279 Cov.: 32 AF XY: 0.0554 AC XY: 4127 AN XY: 74478

Gnomad4 AFR AF: 0.0287

Gnomad4 AMR AF: 0.0568

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.0804

Gnomad4 FIN AF: 0.0573

Gnomad4 NFE AF: 0.0703

Gnomad4 OTH AF: 0.0761

Alfa AF: 0.0634 Hom.: 49

Bravo AF: 0.0535

Asia WGS AF: 0.0450 AC: 157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.22
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs45458507; hg19: chr3-117216421;