chr8-25781517-A-T

Variant names:

• chr8-25781517-A-T
• rs4872354
• XR_001745849.2:n.239-54861A>T

Variant summary

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

The XR_001745849.2(LOC107986933):​n.239-54861A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,106 control chromosomes in the GnomAD database, including 3,389 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 0.20 (3389 hom., cov: 32)
• Consequence: LOC107986933 XR_001745849.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 5 publications found

Genes affected

LOC107986933 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 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: 0.197 AC: 29897 AN: 151988 Hom.: 3377 Cov.: 32

Gnomad AFR AF: 0.0811

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.197 AC: 29925 AN: 152106 Hom.: 3389 Cov.: 32 AF XY: 0.194 AC XY: 14447 AN XY: 74348

African (AFR) AF: 0.0810 AC: 3365 AN: 41528

American (AMR) AF: 0.247 AC: 3770 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3466

East Asian (EAS) AF: 0.205 AC: 1058 AN: 5168

South Asian (SAS) AF: 0.148 AC: 716 AN: 4824

European-Finnish (FIN) AF: 0.238 AC: 2522 AN: 10584

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17178 AN: 67950

Other (OTH) AF: 0.197 AC: 415 AN: 2108

Alfa AF: 0.223 Hom.: 524

Bravo AF: 0.194

Asia WGS AF: 0.212 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.60
DANN	Benign	0.73
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4872354; hg19: chr8-25639033;