12-48285832-T-C

Variant summary

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

The XR_944923.3(LOC105369753):n.375-6381A>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 0.721 in 151,930 control chromosomes in the GnomAD database, including 40,100 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 0.72 (40100 hom., cov: 30)
• Consequence: LOC105369753 XR_944923.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586

Genes affected

LOC105369753 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369753	XR_944923.3	n.375-6381A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109531 AN: 151812 Hom.: 40078 Cov.: 30

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.844

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.721 AC: 109601 AN: 151930 Hom.: 40100 Cov.: 30 AF XY: 0.714 AC XY: 53037 AN XY: 74260

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.727

Alfa AF: 0.735 Hom.: 15699

Bravo AF: 0.712

Asia WGS AF: 0.543 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.7
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1489111; hg19: chr12-48679615;