rs12327091

Positions:

• chr18-43842486-C-A
• chr18-43842486-C-G
• chr18-43842486-C-T

Variant summary

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

The XR_935415.3(LOC105372088):​n.263-31709G>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 0.0822 in 151,482 control chromosomes in the GnomAD database, including 639 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 0.082 (639 hom., cov: 32)
• Consequence: LOC105372088 XR_935415.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771

Genes affected

LOC105372088 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372088	XR_935415.3	n.263-31709G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0823 AC: 12463 AN: 151358 Hom.: 641 Cov.: 32

Gnomad AFR AF: 0.0286

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0987

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0454

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.0983

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0955

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

GnomAD4 genome AF: 0.0822 AC: 12458 AN: 151482 Hom.: 639 Cov.: 32 AF XY: 0.0804 AC XY: 5952 AN XY: 74016

Gnomad4 AFR AF: 0.0286

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0987

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0458

Gnomad4 FIN AF: 0.0925

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0944

Alfa AF: 0.0718 Hom.: 166

Bravo AF: 0.0842

Asia WGS AF: 0.0680 AC: 232 AN: 3420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12327091; hg19: chr18-41422451;