rs79085477

Variant names:

• chr20-57126159-C-T
• rs79085477
• XR_007067759.1:n.277+5836G>A

Variant summary

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

The XR_936901.3(LOC105372685):​n.282+5836G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0223 in 151,688 control chromosomes in the GnomAD database, including 70 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 0.022 (70 hom., cov: 31)
• Consequence: LOC105372685 XR_936901.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.466
• Publications: 5 publications found

Genes affected

LOC105372685 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0526 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: 0.0223 AC: 3376 AN: 151572 Hom.: 69 Cov.: 31

Gnomad AFR AF: 0.0545

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00985

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.0525

Gnomad SAS AF: 0.0312

Gnomad FIN AF: 0.000478

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00745

Gnomad OTH AF: 0.0178

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

GnomAD4 genome AF: 0.0223 AC: 3384 AN: 151688 Hom.: 70 Cov.: 31 AF XY: 0.0216 AC XY: 1601 AN XY: 74086

African (AFR) AF: 0.0545 AC: 2252 AN: 41304

American (AMR) AF: 0.00983 AC: 150 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.00317 AC: 11 AN: 3468

East Asian (EAS) AF: 0.0528 AC: 273 AN: 5166

South Asian (SAS) AF: 0.0310 AC: 149 AN: 4804

European-Finnish (FIN) AF: 0.000478 AC: 5 AN: 10470

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00745 AC: 506 AN: 67916

Other (OTH) AF: 0.0176 AC: 37 AN: 2104

Alfa AF: 0.0173 Hom.: 6

Bravo AF: 0.0242

Asia WGS AF: 0.0830 AC: 288 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.31
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs79085477; hg19: chr20-55701215;