12-131690939-T-G

Variant names:

• chr12-131690939-T-G
• rs1545610
• XR_001749183.1:n.1484+40T>G

Variant summary

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

The XR_001749183.1(LOC105370087):​n.1484+40T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,070 control chromosomes in the GnomAD database, including 10,689 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 0.37 (10689 hom., cov: 32)
• Consequence: LOC105370087 XR_001749183.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 9 publications found

Genes affected

LOC105370087 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56193 AN: 151952 Hom.: 10687 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.370 AC: 56232 AN: 152070 Hom.: 10689 Cov.: 32 AF XY: 0.363 AC XY: 26959 AN XY: 74342

African (AFR) AF: 0.352 AC: 14604 AN: 41470

American (AMR) AF: 0.325 AC: 4972 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1188 AN: 3460

East Asian (EAS) AF: 0.220 AC: 1140 AN: 5192

South Asian (SAS) AF: 0.243 AC: 1171 AN: 4822

European-Finnish (FIN) AF: 0.376 AC: 3976 AN: 10570

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27833 AN: 67958

Other (OTH) AF: 0.366 AC: 773 AN: 2110

Alfa AF: 0.386 Hom.: 35925

Bravo AF: 0.365

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.95
DANN	Benign	0.40
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs1545610; hg19: chr12-132175484;