2-162254026-A-G

Variant names:

• chr2-162254026-A-G
• rs2111485
• XR_923544.3:n.681+3739A>G

Variant summary

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

The XR_923544.3(LOC105373724):​n.681+3739A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,990 control chromosomes in the GnomAD database, including 18,447 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 0.46 (18447 hom., cov: 31)
• Consequence: LOC105373724 XR_923544.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 150 publications found

Genes affected

LOC105373724 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70088 AN: 151872 Hom.: 18450 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.461 AC: 70082 AN: 151990 Hom.: 18447 Cov.: 31 AF XY: 0.455 AC XY: 33825 AN XY: 74300

African (AFR) AF: 0.230 AC: 9540 AN: 41472

American (AMR) AF: 0.443 AC: 6761 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1722 AN: 3470

East Asian (EAS) AF: 0.178 AC: 917 AN: 5166

South Asian (SAS) AF: 0.429 AC: 2067 AN: 4820

European-Finnish (FIN) AF: 0.564 AC: 5951 AN: 10550

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.610 AC: 41453 AN: 67930

Other (OTH) AF: 0.474 AC: 1004 AN: 2116

Alfa AF: 0.556 Hom.: 109565

Bravo AF: 0.438

Asia WGS AF: 0.283 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.70
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs2111485; hg19: chr2-163110536;