20-17817862-A-G

Variant names:

• chr20-17817862-A-G
• rs241141
• XR_001754508.1:n.798-1429T>C

Variant summary

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

The XR_001754508.1(LOC107985440):​n.798-1429T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 151,988 control chromosomes in the GnomAD database, including 38,994 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 0.70 (38994 hom., cov: 30)
• Consequence: LOC107985440 XR_001754508.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.983
• Publications: 1 publications found

Genes affected

LOC107985440 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 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: 0.702 AC: 106585 AN: 151870 Hom.: 38932 Cov.: 30

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.702 AC: 106701 AN: 151988 Hom.: 38994 Cov.: 30 AF XY: 0.703 AC XY: 52229 AN XY: 74294

African (AFR) AF: 0.920 AC: 38149 AN: 41486

American (AMR) AF: 0.664 AC: 10137 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2175 AN: 3466

East Asian (EAS) AF: 0.776 AC: 3991 AN: 5142

South Asian (SAS) AF: 0.652 AC: 3143 AN: 4822

European-Finnish (FIN) AF: 0.634 AC: 6697 AN: 10562

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40360 AN: 67936

Other (OTH) AF: 0.685 AC: 1439 AN: 2102

Alfa AF: 0.610 Hom.: 8245

Bravo AF: 0.717

Asia WGS AF: 0.698 AC: 2429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.36
DANN	Benign	0.51
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs241141; hg19: chr20-17798507;