rs393076

Positions:

• chr3-161384309-A-G

Variant summary

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

The XR_007096152.1(LOC107986150):​n.5333A>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 0.226 in 151,936 control chromosomes in the GnomAD database, including 5,627 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 0.23 (5627 hom., cov: 32)
• Consequence: LOC107986150 XR_007096152.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

Genes affected

LOC107986150 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986150	XR_007096152.1	n.5333A>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: 0.226 AC: 34260 AN: 151818 Hom.: 5610 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.0694

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.226 AC: 34328 AN: 151936 Hom.: 5627 Cov.: 32 AF XY: 0.225 AC XY: 16715 AN XY: 74292

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.0694

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.219

Alfa AF: 0.129 Hom.: 3545

Bravo AF: 0.257

Asia WGS AF: 0.273 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs393076; hg19: chr3-161102097;