XR_007058377.1:n.3327C>A

Variant names:

• chr4-176453492-C-A
• rs309753
• XR_007058377.1:n.3327C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007058377.1(LOC124900817):​n.3327C>A 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 0.827 in 152,152 control chromosomes in the GnomAD database, including 52,157 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 0.83 (52157 hom., cov: 31)
• Consequence: LOC124900817 XR_007058377.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746
• Publications: 2 publications found

Genes affected

LOC124900817 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.88 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: 0.827 AC: 125702 AN: 152034 Hom.: 52111 Cov.: 31

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.827 AC: 125806 AN: 152152 Hom.: 52157 Cov.: 31 AF XY: 0.823 AC XY: 61225 AN XY: 74396

African (AFR) AF: 0.887 AC: 36822 AN: 41490

American (AMR) AF: 0.781 AC: 11931 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3043 AN: 3468

East Asian (EAS) AF: 0.768 AC: 3976 AN: 5180

South Asian (SAS) AF: 0.752 AC: 3626 AN: 4824

European-Finnish (FIN) AF: 0.781 AC: 8278 AN: 10602

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55356 AN: 67988

Other (OTH) AF: 0.809 AC: 1705 AN: 2108

Alfa AF: 0.816 Hom.: 196285

Bravo AF: 0.829

Asia WGS AF: 0.751 AC: 2611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.64
DANN	Benign	0.62
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs309753; hg19: chr4-177374643;