12-54196349-G-A

Variant names:

• chr12-54196349-G-A
• rs2029167
• XR_944983.1:n.367-4111G>A

Variant summary

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

The XR_944983.1(LOC105369777):​n.367-4111G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151,854 control chromosomes in the GnomAD database, including 20,610 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 0.52 (20610 hom., cov: 31)
• Consequence: LOC105369777 XR_944983.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 6 publications found

Genes affected

LOC105369777 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78735 AN: 151736 Hom.: 20600 Cov.: 31

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.519 AC: 78778 AN: 151854 Hom.: 20610 Cov.: 31 AF XY: 0.524 AC XY: 38903 AN XY: 74180

African (AFR) AF: 0.488 AC: 20192 AN: 41384

American (AMR) AF: 0.488 AC: 7441 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1875 AN: 3466

East Asian (EAS) AF: 0.503 AC: 2581 AN: 5128

South Asian (SAS) AF: 0.622 AC: 2999 AN: 4818

European-Finnish (FIN) AF: 0.615 AC: 6473 AN: 10528

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35647 AN: 67954

Other (OTH) AF: 0.501 AC: 1058 AN: 2110

Alfa AF: 0.517 Hom.: 2549

Bravo AF: 0.505

Asia WGS AF: 0.521 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	9.5
DANN	Benign	0.72
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2029167; hg19: chr12-54590133;