3-30605058-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105377015 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377015	XM_047449400.1	c.*839C>G		3_prime_UTR_variant	2/2

Ensembl

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

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

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.773

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.2
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs764522; hg19: chr3-30646550;