chr12-48027624-G-T

Variant names:

• chr12-48027624-G-T
• rs12305182
• XR_001749115.3:n.227-2147G>T

Variant summary

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

The XR_001749115.3(LOC105369750):​n.227-2147G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,008 control chromosomes in the GnomAD database, including 3,984 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 0.23 (3984 hom., cov: 32)
• Consequence: LOC105369750 XR_001749115.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371
• Publications: 5 publications found

Genes affected

LOC105369750 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34184 AN: 151890 Hom.: 3977 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.225 AC: 34202 AN: 152008 Hom.: 3984 Cov.: 32 AF XY: 0.219 AC XY: 16298 AN XY: 74304

African (AFR) AF: 0.217 AC: 8981 AN: 41432

American (AMR) AF: 0.219 AC: 3346 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 977 AN: 3470

East Asian (EAS) AF: 0.278 AC: 1440 AN: 5176

South Asian (SAS) AF: 0.153 AC: 734 AN: 4810

European-Finnish (FIN) AF: 0.143 AC: 1513 AN: 10572

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16483 AN: 67962

Other (OTH) AF: 0.258 AC: 544 AN: 2112

Alfa AF: 0.214 Hom.: 1927

Bravo AF: 0.231

Asia WGS AF: 0.191 AC: 662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs12305182; hg19: chr12-48421407;