20-48399072-A-G

Variant names:

• chr20-48399072-A-G
• rs4809688
• XR_001754655.2:n.2394A>G

Variant summary

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

The XR_936812.3(LOC105372643):​n.2398A>G 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 0.553 in 152,074 control chromosomes in the GnomAD database, including 25,258 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 0.55 (25258 hom., cov: 32)
• Consequence: LOC105372643 XR_936812.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 3 publications found

Genes affected

LOC105372643 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 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: 0.553 AC: 84023 AN: 151956 Hom.: 25210 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.553 AC: 84138 AN: 152074 Hom.: 25258 Cov.: 32 AF XY: 0.546 AC XY: 40575 AN XY: 74340

African (AFR) AF: 0.783 AC: 32487 AN: 41510

American (AMR) AF: 0.617 AC: 9418 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1666 AN: 3472

East Asian (EAS) AF: 0.673 AC: 3471 AN: 5156

South Asian (SAS) AF: 0.413 AC: 1990 AN: 4824

European-Finnish (FIN) AF: 0.328 AC: 3459 AN: 10556

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29870 AN: 67972

Other (OTH) AF: 0.535 AC: 1127 AN: 2106

Alfa AF: 0.480 Hom.: 30589

Bravo AF: 0.593

Asia WGS AF: 0.543 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.49
PhyloP100		-0.074

Splicing

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

Other links and lift over

dbSNP: rs4809688; hg19: chr20-47027815;