13-109787217-G-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124903211 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903211	XM_047430835.1	c.125G>T	p.Gly42Val	missense_variant	Exon 1 of 2		XP_047286791.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000275741	ENST00000615635.1	n.115+1272G>T		intron_variant	Intron 1 of 2	4

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

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.825

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12858484; hg19: chr13-110439564;