rs12289182

Positions:

• chr11-87784122-C-T

Variant summary

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

The XR_002957260.2(LOC107984361):​n.467-67437C>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 0.0474 in 152,188 control chromosomes in the GnomAD database, including 423 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 0.047 (423 hom., cov: 32)
• Consequence: LOC107984361 XR_002957260.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191

Genes affected

LOC107984361 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984361	XR_002957260.2	n.467-67437C>T		intron_variant, non_coding_transcript_variant
LOC107984361	XR_002957261.2	n.390-87094C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0472 AC: 7184 AN: 152070 Hom.: 418 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0379

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.0430

Gnomad FIN AF: 0.00293

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.00722

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0474 AC: 7216 AN: 152188 Hom.: 423 Cov.: 32 AF XY: 0.0466 AC XY: 3468 AN XY: 74394

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0377

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.0242

Gnomad4 SAS AF: 0.0424

Gnomad4 FIN AF: 0.00293

Gnomad4 NFE AF: 0.00725

Gnomad4 OTH AF: 0.0407

Alfa AF: 0.0296 Hom.: 27

Bravo AF: 0.0533

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.97
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12289182; hg19: chr11-87495014;