chr2-128531089-G-A

Variant names:

• chr2-128531089-G-A
• rs2445234
• XR_923318.2:n.2388-90262G>A

Variant summary

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

The XR_923318.2(LOC105373611):​n.2388-90262G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,146 control chromosomes in the GnomAD database, including 7,069 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 0.22 (7069 hom., cov: 32)
• Consequence: LOC105373611 XR_923318.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 1 publications found

Genes affected

LOC105373611 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 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: 0.219 AC: 33225 AN: 152028 Hom.: 7036 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0320

Gnomad SAS AF: 0.0838

Gnomad FIN AF: 0.0562

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.219 AC: 33320 AN: 152146 Hom.: 7069 Cov.: 32 AF XY: 0.213 AC XY: 15834 AN XY: 74404

African (AFR) AF: 0.559 AC: 23180 AN: 41466

American (AMR) AF: 0.143 AC: 2192 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3468

East Asian (EAS) AF: 0.0315 AC: 163 AN: 5172

South Asian (SAS) AF: 0.0845 AC: 408 AN: 4828

European-Finnish (FIN) AF: 0.0562 AC: 596 AN: 10600

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0868 AC: 5907 AN: 68014

Other (OTH) AF: 0.207 AC: 436 AN: 2108

Alfa AF: 0.180 Hom.: 671

Bravo AF: 0.240

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.3
DANN	Benign	0.46
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2445234; hg19: chr2-129288663;