rs55877356

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-17229207-G-C
• chr10-17229207-G-A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_003380.5(VIM):​c.-147-69G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.035 in 353,666 control chromosomes in the GnomAD database, including 211 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.024 (56 hom., cov: 31)
  • Exomes 𝑓: 0.043 (155 hom.)
• Consequence: VIM NM_003380.5 intron
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• 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: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BP6: Variant 10-17229207-G-C is Benign according to our data. Variant chr10-17229207-G-C is described in ClinVar as Likely_benign. ClinVar VariationId is 1316913.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0542 is higher than 0.05.

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>C		intron	N/A	NP_003371.2	P08670
	VIM-AS1	NR_108061.1		n.641+138C>G		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>C		intron	N/A	ENSP00000446007.1	P08670
	VIM	ENST00000881961.1		c.-216G>C		5_prime_UTR	Exon 1 of 9	ENSP00000552020.1
	VIM	ENST00000946784.1		c.-124-92G>C		intron	N/A	ENSP00000616843.1

Frequencies

GnomAD3 genomes AF: 0.0236 AC: 3376 AN: 143280 Hom.: 56 Cov.: 31

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0244

Gnomad ASJ AF: 0.0189

Gnomad EAS AF: 0.000905

Gnomad SAS AF: 0.00692

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.0445

Gnomad NFE AF: 0.0282

Gnomad OTH AF: 0.0255

GnomAD4 exome AF: 0.0427 AC: 8989 AN: 210322 Hom.: 155 Cov.: 4 AF XY: 0.0398 AC XY: 4567 AN XY: 114686

African (AFR) AF: 0.0524 AC: 122 AN: 2328

American (AMR) AF: 0.0335 AC: 271 AN: 8096

Ashkenazi Jewish (ASJ) AF: 0.0464 AC: 217 AN: 4678

East Asian (EAS) AF: 0.000138 AC: 1 AN: 7256

South Asian (SAS) AF: 0.00734 AC: 283 AN: 38544

European-Finnish (FIN) AF: 0.0762 AC: 1069 AN: 14026

Middle Eastern (MID) AF: 0.0690 AC: 53 AN: 768

European-Non Finnish (NFE) AF: 0.0519 AC: 6427 AN: 123776

Other (OTH) AF: 0.0503 AC: 546 AN: 10850

GnomAD4 genome AF: 0.0235 AC: 3375 AN: 143344 Hom.: 56 Cov.: 31 AF XY: 0.0242 AC XY: 1679 AN XY: 69346

African (AFR) AF: 0.0135 AC: 523 AN: 38812

American (AMR) AF: 0.0244 AC: 335 AN: 13746

Ashkenazi Jewish (ASJ) AF: 0.0189 AC: 64 AN: 3394

East Asian (EAS) AF: 0.000908 AC: 4 AN: 4406

South Asian (SAS) AF: 0.00670 AC: 29 AN: 4330

European-Finnish (FIN) AF: 0.0535 AC: 492 AN: 9192

Middle Eastern (MID) AF: 0.0407 AC: 11 AN: 270

European-Non Finnish (NFE) AF: 0.0282 AC: 1866 AN: 66286

Other (OTH) AF: 0.0253 AC: 51 AN: 2014

Alfa AF: 0.00965 Hom.: 0

Bravo AF: 0.0204

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	14
DANN	Benign	0.88
PhyloP100		0.80
PromoterAI		0.031	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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;