10-17218291-A-G

Variant summary

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

The NR_108061.1(VIM-AS1):n.642-2017T>C 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 0.421 in 152,006 control chromosomes in the GnomAD database, including 13,922 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 0.42 (13922 hom., cov: 32)
• Consequence: VIM-AS1 NR_108061.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557

Genes affected

VIM-AS1 (HGNC:44879): (VIM antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VIM-AS1	NR_108061.1	n.642-2017T>C		intron_variant, non_coding_transcript_variant
VIM-AS1	NR_108060.1	n.44-616T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VIM-AS1	ENST00000605833.2	n.675-2017T>C		intron_variant, non_coding_transcript_variant		3
VIM-AS1	ENST00000437232.5	n.44-616T>C		intron_variant, non_coding_transcript_variant		2
VIM-AS1	ENST00000661048.1	n.77-2927T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63988 AN: 151888 Hom.: 13921 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.421 AC: 64019 AN: 152006 Hom.: 13922 Cov.: 32 AF XY: 0.426 AC XY: 31659 AN XY: 74292

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.454

Alfa AF: 0.442 Hom.: 19781

Bravo AF: 0.413

Asia WGS AF: 0.592 AC: 2059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.51
Dann	Benign	0.29
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10904908; hg19: chr10-17260290;