chr20-17173740-G-A

Variant names:

• chr20-17173740-G-A
• rs852102
• XR_937289.1:n.311-139G>A

Variant summary

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

The XR_937289.1(LOC105372544):​n.311-139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,206 control chromosomes in the GnomAD database, including 49,430 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 0.80 (49430 hom., cov: 33)
• Consequence: LOC105372544 XR_937289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 2 publications found

Genes affected

LOC105372544 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.877 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: 0.799 AC: 121529 AN: 152088 Hom.: 49422 Cov.: 33

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.799 AC: 121565 AN: 152206 Hom.: 49430 Cov.: 33 AF XY: 0.795 AC XY: 59191 AN XY: 74422

African (AFR) AF: 0.685 AC: 28455 AN: 41522

American (AMR) AF: 0.716 AC: 10952 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3143 AN: 3472

East Asian (EAS) AF: 0.578 AC: 2983 AN: 5160

South Asian (SAS) AF: 0.747 AC: 3602 AN: 4820

European-Finnish (FIN) AF: 0.917 AC: 9725 AN: 10606

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.883 AC: 60072 AN: 68018

Other (OTH) AF: 0.807 AC: 1706 AN: 2114

Alfa AF: 0.827 Hom.: 10300

Bravo AF: 0.777

Asia WGS AF: 0.645 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.26
DANN	Benign	0.72
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs852102; hg19: chr20-17154385;