XR_001749115.3:n.227-2520A>G

Variant names:

• chr12-48027251-A-G
• rs17122571
• XR_001749115.3:n.227-2520A>G

Variant summary

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

The XR_001749115.3(LOC105369750):​n.227-2520A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0805 in 152,232 control chromosomes in the GnomAD database, including 519 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 0.080 (519 hom., cov: 32)
• Consequence: LOC105369750 XR_001749115.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 11 publications found

Genes affected

LOC105369750 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0818 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: 0.0805 AC: 12242 AN: 152114 Hom.: 519 Cov.: 32

Gnomad AFR AF: 0.0824

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00538

Gnomad SAS AF: 0.0661

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.0828

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

GnomAD4 genome AF: 0.0805 AC: 12248 AN: 152232 Hom.: 519 Cov.: 32 AF XY: 0.0809 AC XY: 6024 AN XY: 74438

African (AFR) AF: 0.0824 AC: 3420 AN: 41526

American (AMR) AF: 0.0595 AC: 911 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 392 AN: 3470

East Asian (EAS) AF: 0.00559 AC: 29 AN: 5188

South Asian (SAS) AF: 0.0661 AC: 319 AN: 4824

European-Finnish (FIN) AF: 0.120 AC: 1277 AN: 10606

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0836 AC: 5687 AN: 68000

Other (OTH) AF: 0.0814 AC: 172 AN: 2112

Alfa AF: 0.0747 Hom.: 204

Bravo AF: 0.0755

Asia WGS AF: 0.0380 AC: 134 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.9
DANN	Benign	0.81
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs17122571; hg19: chr12-48421034;