rs2408954

Variant names:

• chr12-48028706-G-A
• rs2408954
• XR_001749115.3:n.227-1065G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_944904.3(LOC105369750):​n.227-1065G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,004 control chromosomes in the GnomAD database, including 7,254 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 0.28 (7254 hom., cov: 31)
• Consequence: LOC105369750 XR_944904.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 2 publications found

Genes affected

LOC105369750 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 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: 0.279 AC: 42412 AN: 151886 Hom.: 7249 Cov.: 31

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.279 AC: 42453 AN: 152004 Hom.: 7254 Cov.: 31 AF XY: 0.276 AC XY: 20520 AN XY: 74312

African (AFR) AF: 0.480 AC: 19878 AN: 41408

American (AMR) AF: 0.163 AC: 2494 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3470

East Asian (EAS) AF: 0.158 AC: 817 AN: 5172

South Asian (SAS) AF: 0.150 AC: 723 AN: 4816

European-Finnish (FIN) AF: 0.255 AC: 2700 AN: 10568

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14536 AN: 67976

Other (OTH) AF: 0.245 AC: 517 AN: 2110

Alfa AF: 0.261 Hom.: 802

Bravo AF: 0.282

Asia WGS AF: 0.177 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	18
DANN	Benign	0.87
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs2408954; hg19: chr12-48422489;