rs2902940

Variant names:

• chr20-40462847-A-G
• rs2902940
• XR_936718.3:n.1155+1473T>C

Your query was ambiguous. Multiple possible variants found:

• chr20-40462847-A-G
• chr20-40462847-A-T

Variant summary

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

The XR_936718.3(LOC105372618):​n.1155+1473T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,018 control chromosomes in the GnomAD database, including 9,682 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 0.34 (9682 hom., cov: 32)
• Consequence: LOC105372618 XR_936718.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 66 publications found

Genes affected

LOC105372618 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 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: 0.341 AC: 51856 AN: 151900 Hom.: 9662 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.342 AC: 51917 AN: 152018 Hom.: 9682 Cov.: 32 AF XY: 0.334 AC XY: 24790 AN XY: 74310

African (AFR) AF: 0.497 AC: 20606 AN: 41470

American (AMR) AF: 0.299 AC: 4565 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3470

East Asian (EAS) AF: 0.272 AC: 1401 AN: 5160

South Asian (SAS) AF: 0.321 AC: 1545 AN: 4814

European-Finnish (FIN) AF: 0.201 AC: 2125 AN: 10560

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20184 AN: 67948

Other (OTH) AF: 0.300 AC: 632 AN: 2110

Alfa AF: 0.306 Hom.: 22244

Bravo AF: 0.354

Asia WGS AF: 0.312 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	12
DANN	Benign	0.91
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs2902940; hg19: chr20-39091487;