2-55862405-A-G

Variant names:

• chr2-55862405-A-G
• rs1367226
• XR_002959388.2:n.229-11478A>G

Variant summary

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

The XR_002959388.2(LOC112268416):​n.229-11478A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 152,000 control chromosomes in the GnomAD database, including 34,728 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 0.66 (34728 hom., cov: 31)
• Consequence: LOC112268416 XR_002959388.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490
• Publications: 23 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 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: 0.658 AC: 99921 AN: 151882 Hom.: 34687 Cov.: 31

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.658 AC: 100020 AN: 152000 Hom.: 34728 Cov.: 31 AF XY: 0.655 AC XY: 48630 AN XY: 74270

African (AFR) AF: 0.861 AC: 35729 AN: 41476

American (AMR) AF: 0.538 AC: 8208 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2553 AN: 3470

East Asian (EAS) AF: 0.899 AC: 4624 AN: 5142

South Asian (SAS) AF: 0.683 AC: 3293 AN: 4822

European-Finnish (FIN) AF: 0.440 AC: 4646 AN: 10560

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38677 AN: 67948

Other (OTH) AF: 0.674 AC: 1421 AN: 2108

Alfa AF: 0.618 Hom.: 61004

Bravo AF: 0.672

Asia WGS AF: 0.788 AC: 2740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs1367226; hg19: chr2-56089540;