rs11787001

Positions:

• chr8-25741082-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001745849.2(LOC107986933):​n.239-95296C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

LOC107986933 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986933	XR_001745849.2	n.239-95296C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.278

Alfa AF: 0.299 Hom.: 1254

Bravo AF: 0.258

Asia WGS AF: 0.350 AC: 1214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11787001; hg19: chr8-25598598;