12-28123693-T-C

Variant names:

• chr12-28123693-T-C
• rs10843104
• XR_001749450.2:n.76+617T>C

Variant summary

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

The XR_931461.3(LOC105369710):​n.102+5780A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 151,946 control chromosomes in the GnomAD database, including 6,124 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 0.28 (6124 hom., cov: 32)
• Consequence: LOC105369710 XR_931461.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14
• Publications: 10 publications found

Genes affected

LOC107984462 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42385 AN: 151828 Hom.: 6100 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.0873

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.279 AC: 42457 AN: 151946 Hom.: 6124 Cov.: 32 AF XY: 0.273 AC XY: 20290 AN XY: 74284

African (AFR) AF: 0.307 AC: 12712 AN: 41438

American (AMR) AF: 0.192 AC: 2931 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1026 AN: 3464

East Asian (EAS) AF: 0.0881 AC: 455 AN: 5164

South Asian (SAS) AF: 0.170 AC: 821 AN: 4816

European-Finnish (FIN) AF: 0.292 AC: 3078 AN: 10558

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20506 AN: 67938

Other (OTH) AF: 0.277 AC: 585 AN: 2112

Alfa AF: 0.294 Hom.: 22559

Bravo AF: 0.274

Asia WGS AF: 0.138 AC: 485 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.044
DANN	Benign	0.54
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10843104; hg19: chr12-28276626;