XR_002959388.2:n.229-8966T>C

Variant names:

• chr2-55864917-T-C
• rs1346789
• XR_002959388.2:n.229-8966T>C

Variant summary

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

The XR_002959388.2(LOC112268416):​n.229-8966T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,104 control chromosomes in the GnomAD database, including 4,183 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 0.19 (4183 hom., cov: 31)
• Consequence: LOC112268416 XR_002959388.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 13 publications found

Genes affected

LOC112268416 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 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: 0.194 AC: 29509 AN: 151986 Hom.: 4186 Cov.: 31

Gnomad AFR AF: 0.0635

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.194 AC: 29500 AN: 152104 Hom.: 4183 Cov.: 31 AF XY: 0.199 AC XY: 14785 AN XY: 74348

African (AFR) AF: 0.0634 AC: 2634 AN: 41536

American (AMR) AF: 0.207 AC: 3161 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 802 AN: 3464

East Asian (EAS) AF: 0.781 AC: 4031 AN: 5160

South Asian (SAS) AF: 0.280 AC: 1349 AN: 4812

European-Finnish (FIN) AF: 0.183 AC: 1934 AN: 10580

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

European-Non Finnish (NFE) AF: 0.216 AC: 14693 AN: 67976

Other (OTH) AF: 0.224 AC: 471 AN: 2106

Alfa AF: 0.187 Hom.: 418

Bravo AF: 0.193

Asia WGS AF: 0.471 AC: 1635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.83
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1346789; hg19: chr2-56092052;