12-28090647-G-T

Variant names:

• chr12-28090647-G-T
• rs7135493
• XR_931461.3:n.155+16459C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_931461.3(LOC105369710):​n.155+16459C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,910 control chromosomes in the GnomAD database, including 3,940 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 0.22 (3940 hom., cov: 31)
• Consequence: LOC105369710 XR_931461.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940

Genes affected

LOC105369710 (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 = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369710	XR_931461.3	n.155+16459C>A		intron_variant	Intron 2 of 2
LOC105369710	XR_931462.3	n.156-1792C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32846 AN: 151792 Hom.: 3934 Cov.: 31

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.216 AC: 32865 AN: 151910 Hom.: 3940 Cov.: 31 AF XY: 0.221 AC XY: 16384 AN XY: 74234

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.220

Alfa AF: 0.204 Hom.: 6019

Bravo AF: 0.222

Asia WGS AF: 0.318 AC: 1104 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	6.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7135493; hg19: chr12-28243580; COSMIC: COSV101081868;