13-109787217-G-T

Variant names:

• chr13-109787217-G-T
• rs12858484
• XM_047430835.1:c.125G>T

Variant summary

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

The XM_047430835.1(LOC124903211):​c.125G>T​(p.Gly42Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.83 in 151,634 control chromosomes in the GnomAD database, including 52,294 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict 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 (52294 hom., cov: 32)
• Consequence: LOC124903211 XM_047430835.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587
• Publications: 0 publications found

Genes affected

LOC124903211 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000615635.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000275741	ENST00000615635.1	TSL:4	n.115+1272G>T		intron	N/A
	ENSG00000275741	ENST00000772402.1		n.67+1272G>T		intron	N/A
	ENSG00000300524	ENST00000772577.1		n.70-383G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.829 AC: 125679 AN: 151526 Hom.: 52246 Cov.: 32

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.885

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.830 AC: 125781 AN: 151634 Hom.: 52294 Cov.: 32 AF XY: 0.829 AC XY: 61453 AN XY: 74094

African (AFR) AF: 0.820 AC: 33977 AN: 41442

American (AMR) AF: 0.860 AC: 13138 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3024 AN: 3470

East Asian (EAS) AF: 0.672 AC: 3330 AN: 4956

South Asian (SAS) AF: 0.784 AC: 3775 AN: 4814

European-Finnish (FIN) AF: 0.849 AC: 8941 AN: 10526

Middle Eastern (MID) AF: 0.880 AC: 257 AN: 292

European-Non Finnish (NFE) AF: 0.838 AC: 56853 AN: 67852

Other (OTH) AF: 0.825 AC: 1740 AN: 2108

Alfa AF: 0.813 Hom.: 2919

Bravo AF: 0.831

Asia WGS AF: 0.733 AC: 2525 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.2
DANN	Benign	0.51
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs12858484; hg19: chr13-110439564;