10-17229207-G-A

Variant names:

• chr10-17229207-G-A
• rs55877356
• NM_003380.5:c.-147-69G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003380.5(VIM):​c.-147-69G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: VIM NM_003380.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.800
• Publications: 0 publications found

Genes affected

VIM (HGNC:12692): (vimentin) This gene encodes a type III intermediate filament protein. Intermediate filaments, along with microtubules and actin microfilaments, make up the cytoskeleton. The encoded protein is responsible for maintaining cell shape and integrity of the cytoplasm, and stabilizing cytoskeletal interactions. This protein is involved in neuritogenesis and cholesterol transport and functions as an organizer of a number of other critical proteins involved in cell attachment, migration, and signaling. Bacterial and viral pathogens have been shown to attach to this protein on the host cell surface. Mutations in this gene are associated with congenital cataracts in human patients. [provided by RefSeq, Aug 2017]

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003380.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VIM	NM_003380.5	MANE Select	c.-147-69G>A		intron	N/A	NP_003371.2	P08670
	VIM-AS1	NR_108061.1		n.641+138C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VIM	ENST00000544301.7	TSL:1 MANE Select	c.-147-69G>A		intron	N/A	ENSP00000446007.1	P08670
	VIM	ENST00000881961.1		c.-216G>A		5_prime_UTR	Exon 1 of 9	ENSP00000552020.1
	VIM	ENST00000946784.1		c.-124-92G>A		intron	N/A	ENSP00000616843.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 210396 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 114720

African (AFR) AF: 0.00 AC: 0 AN: 2328

American (AMR) AF: 0.00 AC: 0 AN: 8100

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4680

East Asian (EAS) AF: 0.00 AC: 0 AN: 7256

South Asian (SAS) AF: 0.00 AC: 0 AN: 38544

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 14038

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 768

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 123826

Other (OTH) AF: 0.00 AC: 0 AN: 10856

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	15
DANN	Uncertain	0.97
PhyloP100		0.80
PromoterAI		-0.090	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs55877356; hg19: chr10-17271206;