rs4662945

Variant names:

• chr2-129458470-A-G
• rs4662945
• XR_001739710.2:n.84-3483A>G

Variant summary

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

The XR_001739710.2(LOC105373613):​n.84-3483A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 152,098 control chromosomes in the GnomAD database, including 27,337 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 0.59 (27337 hom., cov: 33)
• Consequence: LOC105373613 XR_001739710.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 5 publications found

Genes affected

LOC105373613 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 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: 0.591 AC: 89759 AN: 151980 Hom.: 27288 Cov.: 33

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.591 AC: 89862 AN: 152098 Hom.: 27337 Cov.: 33 AF XY: 0.584 AC XY: 43447 AN XY: 74338

African (AFR) AF: 0.724 AC: 30039 AN: 41512

American (AMR) AF: 0.486 AC: 7432 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2055 AN: 3470

East Asian (EAS) AF: 0.259 AC: 1340 AN: 5178

South Asian (SAS) AF: 0.533 AC: 2568 AN: 4816

European-Finnish (FIN) AF: 0.537 AC: 5666 AN: 10554

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38830 AN: 67966

Other (OTH) AF: 0.584 AC: 1232 AN: 2110

Alfa AF: 0.575 Hom.: 75387

Bravo AF: 0.588

Asia WGS AF: 0.414 AC: 1442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.5
DANN	Benign	0.57
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs4662945; hg19: chr2-130216043;