XR_007096152.1:n.5333A>G

Variant names:

• chr3-161384309-A-G
• rs393076
• XR_007096152.1:n.5333A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

LOC107986150 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.442 AC: 18311 AN: 41432

American (AMR) AF: 0.295 AC: 4493 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 444 AN: 3462

East Asian (EAS) AF: 0.305 AC: 1570 AN: 5140

South Asian (SAS) AF: 0.196 AC: 947 AN: 4824

European-Finnish (FIN) AF: 0.0694 AC: 735 AN: 10598

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7117 AN: 67924

Other (OTH) AF: 0.219 AC: 463 AN: 2112

Alfa AF: 0.151 Hom.: 8569

Bravo AF: 0.257

Asia WGS AF: 0.273 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.58
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs393076; hg19: chr3-161102097;