rs6890173

Variant names:

• chr5-163716979-T-G
• rs6890173
• XR_427816.3:n.192-4133T>G

Variant summary

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

The XR_427816.3(LOC102724458):​n.192-4133T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,234 control chromosomes in the GnomAD database, including 1,843 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 0.15 (1843 hom., cov: 32)
• Consequence: LOC102724458 XR_427816.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 1 publications found

Genes affected

LOC102724458 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 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: 0.152 AC: 23141 AN: 152116 Hom.: 1839 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.152 AC: 23160 AN: 152234 Hom.: 1843 Cov.: 32 AF XY: 0.149 AC XY: 11120 AN XY: 74420

African (AFR) AF: 0.162 AC: 6745 AN: 41538

American (AMR) AF: 0.115 AC: 1762 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3472

East Asian (EAS) AF: 0.00386 AC: 20 AN: 5186

South Asian (SAS) AF: 0.121 AC: 583 AN: 4822

European-Finnish (FIN) AF: 0.145 AC: 1537 AN: 10604

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11447 AN: 67998

Other (OTH) AF: 0.164 AC: 346 AN: 2114

Alfa AF: 0.154 Hom.: 256

Bravo AF: 0.146

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.60
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs6890173; hg19: chr5-163143985;