rs2467698

Variant names:

• chr8-25692675-T-C
• rs2467698
• XR_001745849.2:n.238+62306T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001745849.2(LOC107986933):​n.238+62306T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,186 control chromosomes in the GnomAD database, including 7,696 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 0.30 (7696 hom., cov: 33)
• Consequence: LOC107986933 XR_001745849.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.508
• Publications: 0 publications found

Genes affected

LOC107986933 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 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: 0.304 AC: 46237 AN: 152068 Hom.: 7686 Cov.: 33

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.304 AC: 46284 AN: 152186 Hom.: 7696 Cov.: 33 AF XY: 0.299 AC XY: 22263 AN XY: 74386

African (AFR) AF: 0.436 AC: 18076 AN: 41496

American (AMR) AF: 0.210 AC: 3217 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3472

East Asian (EAS) AF: 0.116 AC: 599 AN: 5178

South Asian (SAS) AF: 0.266 AC: 1286 AN: 4830

European-Finnish (FIN) AF: 0.255 AC: 2699 AN: 10594

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18574 AN: 67992

Other (OTH) AF: 0.291 AC: 615 AN: 2116

Alfa AF: 0.286 Hom.: 813

Bravo AF: 0.303

Asia WGS AF: 0.187 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	17
DANN	Benign	0.70
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs2467698; hg19: chr8-25550191;