chr12-121131831-T-C

Variant names:

• chr12-121131831-T-C
• rs670541
• XR_001749352.3:n.328-4990A>G

Variant summary

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

The XR_001749352.3(LOC105370032):​n.328-4990A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,174 control chromosomes in the GnomAD database, including 57,336 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 0.86 (57336 hom., cov: 31)
• Consequence: LOC105370032 XR_001749352.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 4 publications found

Genes affected

LOC105370032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 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: 0.861 AC: 130992 AN: 152056 Hom.: 57306 Cov.: 31

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.861 AC: 131076 AN: 152174 Hom.: 57336 Cov.: 31 AF XY: 0.865 AC XY: 64319 AN XY: 74396

African (AFR) AF: 0.689 AC: 28578 AN: 41464

American (AMR) AF: 0.900 AC: 13761 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 3318 AN: 3472

East Asian (EAS) AF: 0.941 AC: 4876 AN: 5182

South Asian (SAS) AF: 0.911 AC: 4391 AN: 4822

European-Finnish (FIN) AF: 0.935 AC: 9917 AN: 10604

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.930 AC: 63283 AN: 68016

Other (OTH) AF: 0.880 AC: 1860 AN: 2114

Alfa AF: 0.859 Hom.: 9640

Bravo AF: 0.850

Asia WGS AF: 0.917 AC: 3192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.86
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs670541; hg19: chr12-121569634;