chr2-98748116-C-T

Variant names:

• chr2-98748116-C-T
• rs13391794
• XR_007087150.1:n.416-3204C>T

Variant summary

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

The XR_007087150.1(LOC107985922):​n.416-3204C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,228 control chromosomes in the GnomAD database, including 2,837 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 0.19 (2837 hom., cov: 32)
• Consequence: LOC107985922 XR_007087150.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85
• Publications: 1 publications found

Genes affected

LOC107985922 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.221 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: 0.186 AC: 28271 AN: 152108 Hom.: 2835 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.0897

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.186 AC: 28284 AN: 152228 Hom.: 2837 Cov.: 32 AF XY: 0.184 AC XY: 13660 AN XY: 74418

African (AFR) AF: 0.221 AC: 9180 AN: 41544

American (AMR) AF: 0.205 AC: 3136 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 565 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1099 AN: 5182

South Asian (SAS) AF: 0.233 AC: 1123 AN: 4826

European-Finnish (FIN) AF: 0.0897 AC: 950 AN: 10588

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11572 AN: 68004

Other (OTH) AF: 0.186 AC: 393 AN: 2108

Alfa AF: 0.176 Hom.: 293

Bravo AF: 0.197

Asia WGS AF: 0.230 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.076
DANN	Benign	0.57
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs13391794; hg19: chr2-99364579;