2-82924517-G-C

Variant names:

• chr2-82924517-G-C
• rs4852696
• XR_940305.2:n.560+12735C>G

Variant summary

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

The XR_940305.2(LOC105374832):​n.560+12735C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 151,786 control chromosomes in the GnomAD database, including 39,295 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 0.67 (39295 hom., cov: 32)
• Consequence: LOC105374832 XR_940305.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.738
• Publications: 5 publications found

Genes affected

LOC105374832 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.845 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: 0.671 AC: 101757 AN: 151668 Hom.: 39303 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.670 AC: 101749 AN: 151786 Hom.: 39295 Cov.: 32 AF XY: 0.672 AC XY: 49883 AN XY: 74188

African (AFR) AF: 0.253 AC: 10489 AN: 41406

American (AMR) AF: 0.760 AC: 11544 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2804 AN: 3460

East Asian (EAS) AF: 0.785 AC: 4026 AN: 5128

South Asian (SAS) AF: 0.820 AC: 3960 AN: 4828

European-Finnish (FIN) AF: 0.822 AC: 8676 AN: 10556

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57785 AN: 67906

Other (OTH) AF: 0.718 AC: 1510 AN: 2104

Alfa AF: 0.652 Hom.: 2425

Bravo AF: 0.646

Asia WGS AF: 0.752 AC: 2616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.0
DANN	Benign	0.48
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs4852696; hg19: chr2-83151641;