3-30605058-G-C

Variant names:

• chr3-30605058-G-C
• rs764522
• XM_047449400.1:c.*839C>G

Variant summary

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

The XM_047449400.1(LOC105377015):​c.*839C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 152,126 control chromosomes in the GnomAD database, including 44,767 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 0.76 (44767 hom., cov: 32)
• Consequence: LOC105377015 XM_047449400.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 26 publications found

Genes affected

LOC105377015 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 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: 0.762 AC: 115903 AN: 152008 Hom.: 44740 Cov.: 32

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.762 AC: 115971 AN: 152126 Hom.: 44767 Cov.: 32 AF XY: 0.765 AC XY: 56875 AN XY: 74382

African (AFR) AF: 0.628 AC: 26018 AN: 41450

American (AMR) AF: 0.809 AC: 12369 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2770 AN: 3470

East Asian (EAS) AF: 0.886 AC: 4580 AN: 5168

South Asian (SAS) AF: 0.729 AC: 3519 AN: 4828

European-Finnish (FIN) AF: 0.871 AC: 9227 AN: 10592

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.808 AC: 54934 AN: 68008

Other (OTH) AF: 0.773 AC: 1629 AN: 2108

Alfa AF: 0.747 Hom.: 2405

Bravo AF: 0.755

Asia WGS AF: 0.780 AC: 2712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.65
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs764522; hg19: chr3-30646550;