rs12491921

chr3-106570103-T-C

Variant summary

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

The XR_007095992.1(LOC101929485):n.758-11317A>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 0.435 in 151,700 control chromosomes in the GnomAD database, including 14,762 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 0.44 (14762 hom., cov: 30)
• Consequence: LOC101929485 XR_007095992.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799

Genes affected

LOC101929485 (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 = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929485	XR_007095992.1	n.758-11317A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66021 AN: 151576 Hom.: 14760 Cov.: 30

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.435 AC: 66054 AN: 151700 Hom.: 14762 Cov.: 30 AF XY: 0.434 AC XY: 32159 AN XY: 74072

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.439

Alfa AF: 0.474 Hom.: 25550

Bravo AF: 0.426

Asia WGS AF: 0.296 AC: 1031 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	0.88
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12491921; hg19: chr3-106288950;