rs1846090

chr18-14583729-T-C

Variant summary

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

The XR_935172.2(LOC105372004):n.689-6545A>G 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 0.297 in 151,896 control chromosomes in the GnomAD database, including 7,212 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 (7212 hom., cov: 31)
• Consequence: LOC105372004 XR_935172.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.866

Genes affected

LOC105372004 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372004	XR_935172.2	n.689-6545A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45056 AN: 151778 Hom.: 7206 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.297 AC: 45081 AN: 151896 Hom.: 7212 Cov.: 31 AF XY: 0.293 AC XY: 21726 AN XY: 74234

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.291

Alfa AF: 0.341 Hom.: 4241

Bravo AF: 0.285

Asia WGS AF: 0.227 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	6.9
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1846090; hg19: chr18-14583728;