12-121132540-A-G

Variant names:

• chr12-121132540-A-G
• rs684201
• XR_001749352.3:n.328-5699T>C

Variant summary

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

The XR_001749352.3(LOC105370032):​n.328-5699T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,162 control chromosomes in the GnomAD database, including 60,809 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 0.89 (60809 hom., cov: 31)
• Consequence: LOC105370032 XR_001749352.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.951 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: 0.889 AC: 135186 AN: 152046 Hom.: 60774 Cov.: 31

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.953

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.957

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.889 AC: 135272 AN: 152162 Hom.: 60809 Cov.: 31 AF XY: 0.888 AC XY: 66021 AN XY: 74382

African (AFR) AF: 0.756 AC: 31352 AN: 41470

American (AMR) AF: 0.953 AC: 14563 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3357 AN: 3472

East Asian (EAS) AF: 0.741 AC: 3835 AN: 5178

South Asian (SAS) AF: 0.873 AC: 4203 AN: 4814

European-Finnish (FIN) AF: 0.921 AC: 9762 AN: 10604

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.957 AC: 65084 AN: 68028

Other (OTH) AF: 0.922 AC: 1943 AN: 2108

Alfa AF: 0.910 Hom.: 8177

Bravo AF: 0.887

Asia WGS AF: 0.803 AC: 2794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.42
PhyloP100		0.27
PromoterAI		0.036	Neutral

Splicing

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

Other links and lift over

dbSNP: rs684201; hg19: chr12-121570343;