rs10496382

Variant names:

• chr2-104120276-C-T
• rs10496382
• XR_923127.1:n.541+4864G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_923127.1(LOC105373523):​n.541+4864G>A variant causes a intron change. The variant allele was found at a frequency of 0.0683 in 152,152 control chromosomes in the GnomAD database, including 386 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 0.068 (386 hom., cov: 32)
• Consequence: LOC105373523 XR_923127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.60
• Publications: 0 publications found

Genes affected

LOC105373523 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0855 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: 0.0683 AC: 10380 AN: 152034 Hom.: 385 Cov.: 32

Gnomad AFR AF: 0.0878

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.0586

Gnomad ASJ AF: 0.0838

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.0970

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0579

Gnomad OTH AF: 0.0747

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

GnomAD4 genome AF: 0.0683 AC: 10388 AN: 152152 Hom.: 386 Cov.: 32 AF XY: 0.0688 AC XY: 5115 AN XY: 74370

African (AFR) AF: 0.0878 AC: 3647 AN: 41514

American (AMR) AF: 0.0583 AC: 891 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0838 AC: 291 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5170

South Asian (SAS) AF: 0.0762 AC: 367 AN: 4818

European-Finnish (FIN) AF: 0.0970 AC: 1027 AN: 10584

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0579 AC: 3937 AN: 68002

Other (OTH) AF: 0.0739 AC: 156 AN: 2110

Alfa AF: 0.0622 Hom.: 405

Bravo AF: 0.0654

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	20
DANN	Benign	0.81
PhyloP100		5.6

Splicing

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

Other links and lift over

dbSNP: rs10496382; hg19: chr2-104736734;