rs1843834

Variant names:

• chr2-224693325-A-G
• rs1843834
• XR_923956.2:n.289+35A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-224693325-A-G
• chr2-224693325-A-T

Variant summary

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

The XR_923956.2(LOC105373910):​n.289+35A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 151,984 control chromosomes in the GnomAD database, including 38,262 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 0.71 (38262 hom., cov: 30)
• Consequence: LOC105373910 XR_923956.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.729
• Publications: 4 publications found

Genes affected

LOC105373910 (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 (EAS) allele frequency at 95% confidence interval = 0.81 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: 0.705 AC: 107102 AN: 151866 Hom.: 38228 Cov.: 30

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.705 AC: 107190 AN: 151984 Hom.: 38262 Cov.: 30 AF XY: 0.702 AC XY: 52161 AN XY: 74286

African (AFR) AF: 0.815 AC: 33798 AN: 41456

American (AMR) AF: 0.635 AC: 9680 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2163 AN: 3470

East Asian (EAS) AF: 0.831 AC: 4302 AN: 5176

South Asian (SAS) AF: 0.730 AC: 3515 AN: 4812

European-Finnish (FIN) AF: 0.647 AC: 6818 AN: 10538

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44608 AN: 67960

Other (OTH) AF: 0.688 AC: 1455 AN: 2116

Alfa AF: 0.679 Hom.: 27098

Bravo AF: 0.709

Asia WGS AF: 0.746 AC: 2593 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	1.1
DANN	Benign	0.41
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs1843834; hg19: chr2-225558042;