rs10858945

chr12-90049705-A-G

Variant summary

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

The ENST00000651272.1(ENSG00000258216):n.571-44731A>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 0.484 in 151,840 control chromosomes in the GnomAD database, including 18,305 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 0.48 (18305 hom., cov: 30)
• Consequence: ENST00000651272.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837

Genes affected

(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 (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369890	XR_001749246.2	n.1019-17291A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651272.1	n.571-44731A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73430 AN: 151722 Hom.: 18295 Cov.: 30

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.484 AC: 73465 AN: 151840 Hom.: 18305 Cov.: 30 AF XY: 0.484 AC XY: 35911 AN XY: 74206

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.489

Alfa AF: 0.461 Hom.: 35701

Bravo AF: 0.487

Asia WGS AF: 0.554 AC: 1927 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	1.9
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10858945; hg19: chr12-90443482;