chr20-55818377-C-T

Variant names:

• chr20-55818377-C-T
• rs6024454
• XR_936887.2:n.84-8382C>T

Variant summary

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

The XR_936887.2(LOC105372677):​n.84-8382C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,018 control chromosomes in the GnomAD database, including 11,069 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 0.33 (11069 hom., cov: 32)
• Consequence: LOC105372677 XR_936887.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538
• Publications: 1 publications found

Genes affected

LOC105372677 (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 = 0.638 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: 0.325 AC: 49385 AN: 151900 Hom.: 11039 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.325 AC: 49460 AN: 152018 Hom.: 11069 Cov.: 32 AF XY: 0.321 AC XY: 23814 AN XY: 74294

African (AFR) AF: 0.644 AC: 26699 AN: 41446

American (AMR) AF: 0.207 AC: 3163 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1056 AN: 3464

East Asian (EAS) AF: 0.151 AC: 779 AN: 5172

South Asian (SAS) AF: 0.233 AC: 1120 AN: 4816

European-Finnish (FIN) AF: 0.201 AC: 2125 AN: 10568

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13618 AN: 67962

Other (OTH) AF: 0.300 AC: 634 AN: 2112

Alfa AF: 0.237 Hom.: 3776

Bravo AF: 0.338

Asia WGS AF: 0.222 AC: 772 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.91
DANN	Benign	0.66
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs6024454; hg19: chr20-54393433;