2-104119794-C-G

Variant names:

• chr2-104119794-C-G
• rs10189155
• XR_923127.1:n.542-4508G>C

Variant summary

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

The XR_923127.1(LOC105373523):​n.542-4508G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,032 control chromosomes in the GnomAD database, including 1,984 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 0.12 (1984 hom., cov: 33)
• Consequence: LOC105373523 XR_923127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 1 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 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: 0.123 AC: 18640 AN: 151912 Hom.: 1983 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.0602

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.0993

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

GnomAD4 genome AF: 0.123 AC: 18648 AN: 152032 Hom.: 1984 Cov.: 33 AF XY: 0.127 AC XY: 9455 AN XY: 74286

African (AFR) AF: 0.214 AC: 8856 AN: 41450

American (AMR) AF: 0.166 AC: 2532 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0646 AC: 224 AN: 3470

East Asian (EAS) AF: 0.443 AC: 2287 AN: 5164

South Asian (SAS) AF: 0.213 AC: 1025 AN: 4820

European-Finnish (FIN) AF: 0.0602 AC: 636 AN: 10564

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0415 AC: 2820 AN: 67976

Other (OTH) AF: 0.100 AC: 211 AN: 2106

Alfa AF: 0.0187 Hom.: 18

Bravo AF: 0.137

Asia WGS AF: 0.283 AC: 981 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.32
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs10189155; hg19: chr2-104736252;