chr12-131252268-C-T

Variant names:

• chr12-131252268-C-T
• rs4759885
• XR_945558.3:n.890+9107G>A

Variant summary

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

The XR_945558.3(LOC105370082):​n.890+9107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,960 control chromosomes in the GnomAD database, including 10,827 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 0.35 (10827 hom., cov: 32)
• Consequence: LOC105370082 XR_945558.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 2 publications found

Genes affected

LOC105370082 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.25).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.621 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: 0.351 AC: 53316 AN: 151842 Hom.: 10830 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.351 AC: 53307 AN: 151960 Hom.: 10827 Cov.: 32 AF XY: 0.357 AC XY: 26484 AN XY: 74268

African (AFR) AF: 0.165 AC: 6838 AN: 41504

American (AMR) AF: 0.329 AC: 5023 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1444 AN: 3462

East Asian (EAS) AF: 0.639 AC: 3300 AN: 5162

South Asian (SAS) AF: 0.384 AC: 1847 AN: 4816

European-Finnish (FIN) AF: 0.532 AC: 5615 AN: 10546

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28049 AN: 67908

Other (OTH) AF: 0.359 AC: 757 AN: 2110

Alfa AF: 0.386 Hom.: 21938

Bravo AF: 0.328

Asia WGS AF: 0.485 AC: 1684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.3
CADD	Benign	0.18
DANN	Benign	0.38
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4759885; hg19: chr12-131736813;