2-45650417-C-T

Variant names:

• chr2-45650417-C-T
• rs608139
• XR_005647118.2:n.797G>A

Variant summary

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

The XR_005647118.2(LOC102724965):​n.797G>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 0.838 in 152,242 control chromosomes in the GnomAD database, including 53,463 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 0.84 (53463 hom., cov: 35)
• Consequence: LOC102724965 XR_005647118.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177
• Publications: 6 publications found

Genes affected

LOC102724965 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 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: 0.838 AC: 127442 AN: 152124 Hom.: 53449 Cov.: 35

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.838 AC: 127506 AN: 152242 Hom.: 53463 Cov.: 35 AF XY: 0.837 AC XY: 62260 AN XY: 74424

African (AFR) AF: 0.803 AC: 33367 AN: 41530

American (AMR) AF: 0.862 AC: 13197 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3058 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4499 AN: 5166

South Asian (SAS) AF: 0.859 AC: 4144 AN: 4826

European-Finnish (FIN) AF: 0.812 AC: 8607 AN: 10600

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57841 AN: 68014

Other (OTH) AF: 0.835 AC: 1767 AN: 2116

Alfa AF: 0.849 Hom.: 54344

Bravo AF: 0.839

Asia WGS AF: 0.869 AC: 3022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.9
DANN	Benign	0.90
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs608139; hg19: chr2-45877556;