XR_923127.1:n.542-4902A>G

Variant names:

• chr2-104120188-T-C
• rs17029579
• XR_923127.1:n.542-4902A>G

Variant summary

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

The XR_923127.1(LOC105373523):​n.542-4902A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0886 in 152,240 control chromosomes in the GnomAD database, including 1,021 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 0.089 (1021 hom., cov: 32)
• Consequence: LOC105373523 XR_923127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 0 publications found

Genes affected

LOC105373523 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 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: 0.0886 AC: 13473 AN: 152122 Hom.: 1017 Cov.: 32

Gnomad AFR AF: 0.0211

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.0706

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0950

Gnomad OTH AF: 0.0841

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

GnomAD4 genome AF: 0.0886 AC: 13482 AN: 152240 Hom.: 1021 Cov.: 32 AF XY: 0.0924 AC XY: 6875 AN XY: 74432

African (AFR) AF: 0.0210 AC: 873 AN: 41568

American (AMR) AF: 0.126 AC: 1926 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0432 AC: 150 AN: 3472

East Asian (EAS) AF: 0.411 AC: 2127 AN: 5180

South Asian (SAS) AF: 0.0709 AC: 342 AN: 4824

European-Finnish (FIN) AF: 0.125 AC: 1329 AN: 10602

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0951 AC: 6464 AN: 67992

Other (OTH) AF: 0.0828 AC: 175 AN: 2114

Alfa AF: 0.0932 Hom.: 287

Bravo AF: 0.0892

Asia WGS AF: 0.210 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.60
DANN	Benign	0.74
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs17029579; hg19: chr2-104736646;