20-17844499-T-C

Variant names:

• chr20-17844499-T-C
• rs2077147
• XR_001754511.2:n.226+5666A>G

Variant summary

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

The XR_001754511.2(LOC107985440):​n.226+5666A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,304 control chromosomes in the GnomAD database, including 12,757 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 0.40 (12757 hom., cov: 31)
• Consequence: LOC107985440 XR_001754511.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 13 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 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: 0.396 AC: 59855 AN: 151186 Hom.: 12747 Cov.: 31

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.396 AC: 59889 AN: 151304 Hom.: 12757 Cov.: 31 AF XY: 0.392 AC XY: 28993 AN XY: 73966

African (AFR) AF: 0.530 AC: 21616 AN: 40772

American (AMR) AF: 0.366 AC: 5588 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 945 AN: 3466

East Asian (EAS) AF: 0.483 AC: 2497 AN: 5166

South Asian (SAS) AF: 0.238 AC: 1142 AN: 4808

European-Finnish (FIN) AF: 0.356 AC: 3762 AN: 10564

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23128 AN: 67952

Other (OTH) AF: 0.359 AC: 758 AN: 2110

Alfa AF: 0.356 Hom.: 24652

Bravo AF: 0.412

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.6
DANN	Benign	0.69
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs2077147; hg19: chr20-17825143;