20-17155501-C-T

Variant names:

• chr20-17155501-C-T
• rs708983
• XR_937289.1:n.311-18378C>T

Variant summary

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

The XR_937289.1(LOC105372544):​n.311-18378C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 151,898 control chromosomes in the GnomAD database, including 32,398 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 0.63 (32398 hom., cov: 30)
• Consequence: LOC105372544 XR_937289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.500
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.754 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: 0.633 AC: 96043 AN: 151782 Hom.: 32397 Cov.: 30

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.632 AC: 96065 AN: 151898 Hom.: 32398 Cov.: 30 AF XY: 0.633 AC XY: 46987 AN XY: 74240

African (AFR) AF: 0.388 AC: 16058 AN: 41408

American (AMR) AF: 0.616 AC: 9393 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2445 AN: 3464

East Asian (EAS) AF: 0.577 AC: 2958 AN: 5126

South Asian (SAS) AF: 0.583 AC: 2804 AN: 4808

European-Finnish (FIN) AF: 0.820 AC: 8679 AN: 10578

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51628 AN: 67952

Other (OTH) AF: 0.657 AC: 1386 AN: 2108

Alfa AF: 0.614 Hom.: 3177

Bravo AF: 0.608

Asia WGS AF: 0.545 AC: 1898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.82
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs708983; hg19: chr20-17136146;