chr12-11191389-A-G

Variant names:

• chr12-11191389-A-G
• rs7132674
• XR_007063209.1:n.760+1278A>G

Variant summary

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

The XR_007063209.1(LOC107987435):​n.760+1278A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 152,114 control chromosomes in the GnomAD database, including 22,062 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 0.51 (22062 hom., cov: 33)
• Consequence: LOC107987435 XR_007063209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 22 publications found

Genes affected

LOC107987435 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 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: 0.508 AC: 77147 AN: 151996 Hom.: 22058 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.507 AC: 77159 AN: 152114 Hom.: 22062 Cov.: 33 AF XY: 0.515 AC XY: 38297 AN XY: 74370

African (AFR) AF: 0.222 AC: 9223 AN: 41490

American (AMR) AF: 0.597 AC: 9119 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2258 AN: 3468

East Asian (EAS) AF: 0.742 AC: 3827 AN: 5156

South Asian (SAS) AF: 0.649 AC: 3125 AN: 4818

European-Finnish (FIN) AF: 0.666 AC: 7049 AN: 10584

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40583 AN: 67998

Other (OTH) AF: 0.545 AC: 1152 AN: 2112

Alfa AF: 0.563 Hom.: 52687

Bravo AF: 0.491

Asia WGS AF: 0.652 AC: 2265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.42
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs7132674; hg19: chr12-11344304;