chr2-120551912-C-T

Variant names:

• chr2-120551912-C-T
• rs2030746
• XR_001739681.3:n.2105G>A

Variant summary

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

The XR_001739681.3(LOC105373585):​n.2105G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 152,056 control chromosomes in the GnomAD database, including 14,805 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 0.44 (14805 hom., cov: 32)
• Consequence: LOC105373585 XR_001739681.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 61 publications found

Genes affected

LOC105373585 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 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: 0.438 AC: 66516 AN: 151936 Hom.: 14769 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.438 AC: 66600 AN: 152056 Hom.: 14805 Cov.: 32 AF XY: 0.435 AC XY: 32310 AN XY: 74312

African (AFR) AF: 0.510 AC: 21129 AN: 41454

American (AMR) AF: 0.426 AC: 6514 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1481 AN: 3470

East Asian (EAS) AF: 0.481 AC: 2486 AN: 5164

South Asian (SAS) AF: 0.396 AC: 1904 AN: 4810

European-Finnish (FIN) AF: 0.356 AC: 3772 AN: 10586

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27861 AN: 67976

Other (OTH) AF: 0.452 AC: 950 AN: 2104

Alfa AF: 0.420 Hom.: 63199

Bravo AF: 0.445

Asia WGS AF: 0.487 AC: 1692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.33
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2030746; hg19: chr2-121309488;