rs11787001

Variant names:

• chr8-25741082-C-T
• rs11787001
• XR_001745849.2:n.239-95296C>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.239-95296C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,046 control chromosomes in the GnomAD database, including 6,168 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 0.27 (6168 hom., cov: 31)
• Consequence: LOC107986933 XR_001745849.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 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: 0.267 AC: 40569 AN: 151928 Hom.: 6166 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.267 AC: 40574 AN: 152046 Hom.: 6168 Cov.: 31 AF XY: 0.273 AC XY: 20307 AN XY: 74312

African (AFR) AF: 0.116 AC: 4835 AN: 41518

American (AMR) AF: 0.351 AC: 5356 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3472

East Asian (EAS) AF: 0.431 AC: 2225 AN: 5164

South Asian (SAS) AF: 0.283 AC: 1366 AN: 4822

European-Finnish (FIN) AF: 0.370 AC: 3904 AN: 10542

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.309 AC: 21022 AN: 67956

Other (OTH) AF: 0.278 AC: 586 AN: 2108

Alfa AF: 0.294 Hom.: 1258

Bravo AF: 0.258

Asia WGS AF: 0.350 AC: 1214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.56
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs11787001; hg19: chr8-25598598;